PMID-sentid	Pub_year	Sent_text	compound_name	comp_offset	prot_official_name	organism	prot_offset
27284594-1	2016	A chiral N,N"-dioxide/Ni(OTf)2 complex-catalyzed asymmetric Diels-Alder reaction of cyclopentadiene with 2,3-dioxopyrrolidines and 2-alkenoyl pyridines has been achieved.	Cyclopentanes	84-99	POU class 2 homeobox 2	Homo sapiens	25-30
28409626-5	2017	No observation of oligomers or polymers of styrene and high stereoselectivity for the radical addition reaction of CCl4 to cyclopentene suggested that the C-C bond formation proceeded inside the coordination sphere of niobium, which was in good accordance with the negative entropy value of the radical addition reaction.	Cyclopentanes	123-135	C-C motif chemokine ligand 4	Homo sapiens	115-119
27723211-3	2016	The high value of the aza-Piancatelli rearrangement was demonstrated by the synthesis of a cyclopentane-based hNK1 antagonist analogue.	Cyclopentanes	91-103	beta-1,3-glucuronyltransferase 1	Homo sapiens	110-114
26418579-4	2015	Chirooptical properties revealed a beta-turn arrangement of all the synthesized compounds, where, depending on the absolute configuration of the cyclopentane spacer, they can be labeled as left- or right-handed turns.	Cyclopentanes	145-157	amyloid beta precursor protein	Homo sapiens	33-39
27358502-1	2016	ABSTRACT: B3LYP/6-31++G(d) calculations indicated that the reaction of (2E)-3-phenyl-2-nitroprop-2-enenitrile with cyclopentadiene catalyzed by cations of 1,3-dialkylimidazolium ionic liquid shall not take place according to the classical scheme of one-step [2+4] Diels-Alder cycloaddition.	Cyclopentanes	115-130	protein tyrosine phosphatase non-receptor type 22	Homo sapiens	12-15
25575249-1	2015	An unusual room temperature beta-lactone decarboxylation facilitated a five-step enantioselective formal synthesis of the cyclopentane core of an estrogen receptor beta-agonist.	Cyclopentanes	122-134	estrogen receptor 2	Homo sapiens	146-168
25908237-2	2015	Its complex with Cu(OTf)(2) , i.e., Cu(II)-PA, was employed to catalyze the homogeneous Diels-Alder (D-A) reaction of alkenoyl pyridine N-oxides with cyclopentadiene in tetrahydrofuran.	Cyclopentanes	150-165	POU class 2 homeobox 2	Homo sapiens	17-26
25793444-5	2015	The cyclopentene obtained from the PPh3-catalyzed reaction of allenoate H2C C CH(COO-t-Bu) with enynal undergoes decarboxylation under the [Au]/[Ag] catalysis and forms a carboxylate-free benzofuran.	Cyclopentanes	4-16	protein phosphatase 4 catalytic subunit	Homo sapiens	35-39
26204240-0	2015	Excited-State Photolytic Mechanism of Cyclopentene Containing a Group 14 Element: An MP2-CAS//CASSCF Study.	Cyclopentanes	38-50	BCAR1 scaffold protein, Cas family member	Homo sapiens	89-92
23980424-3	2013	The alpha-chain was introduced to the cyclopentane ring via the S(N)2 type nucleophilic substitution of (1S,2R,3R,2"Z)-3-acetoxy-2-(pent-2"-enyl)cyclopent-4-ene-1-ol with a dialkylcuprate for (+)-12-oxo-PDA.	Cyclopentanes	38-50	Fc gamma receptor and transporter	Homo sapiens	4-15
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	Janus kinase 3	Homo sapiens	92-96
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	interferon gamma	Homo sapiens	140-148
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	interleukin 2	Homo sapiens	166-169
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	Janus kinase 3	Homo sapiens	242-246
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	Janus kinase 1	Homo sapiens	247-251
25453808-3	2014	Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNgamma production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2.	Cyclopentanes	50-62	Janus kinase 2	Homo sapiens	272-276
24486198-1	2014	The Yb(OTf)3 catalyzed formal aza-Diels-Alder (or Povarov) reaction of cyclopentadiene and 1,3-cyclohexadiene with in situ-generated N-arylimines under conventional/ultrasonic techniques is herein described.	Cyclopentanes	71-86	POU class 5 homeobox 1	Homo sapiens	7-12
24144235-0	2013	Theoretical study of salt effects on the Diels-Alder reaction of cyclopentadiene with methyl vinyl ketone using RISM-SCF theory.	Cyclopentanes	65-80	KIT ligand	Homo sapiens	117-120
24144235-1	2013	Salt effects on the Diels-Alder reaction of cyclopentadiene with methyl vinyl ketone are investigated using reference interaction site model self-consistent field (RISM-SCF) theory.	Cyclopentanes	44-59	KIT ligand	Homo sapiens	169-172
24366160-1	2014	Geometry optimization for RuX(PPh3)(NHCPh2)(L) (X=hydridotris(pyrazolyl)borate (Tp) and cyclopentadiene (Cp); L=Cl and N3) are investigated by using density functional theory (DFT) with DZVP2/DZVP all-electron mixed basis sets and compared with available experimental values, and the calculated structures are in very good agreement with experimental data.	Cyclopentanes	88-103	protein phosphatase 4 catalytic subunit	Homo sapiens	30-34
23944192-1	2013	Much higher reactivity of [Li(+)@C60]PF6(-) for Diels-Alder cycloaddition toward cyclopentadiene (CpH), in comparison with that of empty C60, was observed.	Cyclopentanes	81-96	carboxypeptidase E	Homo sapiens	98-101
23631440-4	2013	Our previous work with the mercaptosulfide functionality attached to both cyclopentane and pyrrolidine frameworks demonstrated that the cis-(3S,4R)-stereochemistry was optimal for all of the MMPs tested.	Cyclopentanes	74-86	matrix metallopeptidase 1	Homo sapiens	191-195
23261716-11	2013	Our data thus confirm that the new enzymatic assays with two cyclopentane substrates CBP-ol and CBP-one, and especially reduction of CBCP-one with NADPH, are appropriate for the evaluation of AKR1C inhibitors.	Cyclopentanes	61-73	CREB binding protein	Homo sapiens	85-88
23795283-2	2013	We report an efficient synthesis of a cyclopentane-containing compound that potently and selectively inhibits DOT1L (Ki = 1.1 nM) as well as H3K79 methylation (IC50 ~ 200 nM).	Cyclopentanes	38-50	DOT1 like histone lysine methyltransferase	Homo sapiens	110-115
20448048-5	2010	Unlike the PGE(2) receptor, however, the hydroxyl group at C11 in a cyclopentane ring is not essential for OAT-PG substrates.	Cyclopentanes	68-80	polymerase (RNA) III (DNA directed) polypeptide K	Mus musculus	59-62
22924670-0	2012	Stereoselective arylation of substituted cyclopentenes by substrate-directable Heck-Matsuda reactions: a concise total synthesis of the sphingosine 1-phosphate receptor (S1P(1)) agonist VPC01091.	Cyclopentanes	41-54	sphingosine-1-phosphate receptor 1	Homo sapiens	170-176
22364202-3	2012	The selectivity is induced in the cyclization step, and while the enantioselectivity results from the syn/anti orientation around the C-N enamine bond, the diastereoselectivity mainly results from the syn/anti configuration of the substituents in the forming cyclopentane ring.	Cyclopentanes	259-271	synemin	Homo sapiens	102-105
22364202-3	2012	The selectivity is induced in the cyclization step, and while the enantioselectivity results from the syn/anti orientation around the C-N enamine bond, the diastereoselectivity mainly results from the syn/anti configuration of the substituents in the forming cyclopentane ring.	Cyclopentanes	259-271	synemin	Homo sapiens	201-204
22076737-4	2011	In the copolymerization of E with cyclopentene (CPE), for example by the action of 9, the presence of CPE resulted in a dramatic increase in the polymerization activity of E, while CPE incorporation remained close to or at zero.	Cyclopentanes	34-46	carboxypeptidase E	Homo sapiens	48-51
22076737-4	2011	In the copolymerization of E with cyclopentene (CPE), for example by the action of 9, the presence of CPE resulted in a dramatic increase in the polymerization activity of E, while CPE incorporation remained close to or at zero.	Cyclopentanes	34-46	carboxypeptidase E	Homo sapiens	102-105
22076737-4	2011	In the copolymerization of E with cyclopentene (CPE), for example by the action of 9, the presence of CPE resulted in a dramatic increase in the polymerization activity of E, while CPE incorporation remained close to or at zero.	Cyclopentanes	34-46	carboxypeptidase E	Homo sapiens	102-105
19772920-2	2009	Cyclopentane- and cyclohexane-fused pyrazoles with p-hydroxyphenyl rings at positions 1 and 3 displayed modest ERbeta-binding selectivity and variable agonism through ERalpha, while behaving as full estrogen antagonists through ERbeta in estrogen-responsive element (ERE)-dependent gene expression assays.	Cyclopentanes	0-12	estrogen receptor 2	Homo sapiens	111-117
19762008-3	2009	Crystals of 2 are monoclinic, with space group P2(1), the cyclopentane and pyran rings also adopt the envelope conformation.	Cyclopentanes	58-70	cyclin dependent kinase inhibitor 1A	Homo sapiens	47-52
19772920-2	2009	Cyclopentane- and cyclohexane-fused pyrazoles with p-hydroxyphenyl rings at positions 1 and 3 displayed modest ERbeta-binding selectivity and variable agonism through ERalpha, while behaving as full estrogen antagonists through ERbeta in estrogen-responsive element (ERE)-dependent gene expression assays.	Cyclopentanes	0-12	estrogen receptor 1	Homo sapiens	167-174
19772920-2	2009	Cyclopentane- and cyclohexane-fused pyrazoles with p-hydroxyphenyl rings at positions 1 and 3 displayed modest ERbeta-binding selectivity and variable agonism through ERalpha, while behaving as full estrogen antagonists through ERbeta in estrogen-responsive element (ERE)-dependent gene expression assays.	Cyclopentanes	0-12	estrogen receptor 2	Homo sapiens	228-234
19072701-1	2009	N-Cbz- and Boc-protected spirocyclic dienes were prepared by dialkylation of cyclopentadiene.	Cyclopentanes	77-92	BOC cell adhesion associated, oncogene regulated	Homo sapiens	11-14
19390879-5	2009	Binding experiments demonstrate that cyclopentadiene-Ti(IV) moieties, resulting from titanocene dichloride at physiological pH, are bound mainly to different types of collagens and to a lesser extent to casein or bovine serum albumin, forming soluble and stable adducts.	Cyclopentanes	37-52	albumin	Homo sapiens	220-233
19237229-0	2009	New cyclopentane derivatives as inhibitors of steroid metabolizing enzymes AKR1C1 and AKR1C3.	Cyclopentanes	4-16	aldo-keto reductase family 1 member C1	Homo sapiens	75-81
19237229-0	2009	New cyclopentane derivatives as inhibitors of steroid metabolizing enzymes AKR1C1 and AKR1C3.	Cyclopentanes	4-16	aldo-keto reductase family 1 member C3	Homo sapiens	86-92
19237229-1	2009	A series of cyclopentane derivatives was synthesized and evaluated for inhibition of the steroid metabolizing enzymes AKR1C1 and AKR1C3.	Cyclopentanes	12-24	aldo-keto reductase family 1 member C1	Homo sapiens	118-124
19237229-1	2009	A series of cyclopentane derivatives was synthesized and evaluated for inhibition of the steroid metabolizing enzymes AKR1C1 and AKR1C3.	Cyclopentanes	12-24	aldo-keto reductase family 1 member C3	Homo sapiens	129-135
18954109-1	2008	5-Alkoxyfuran-2(5H)-ones and their optically pure 3-p-tolylsulfinyl derivatives, synthetic equivalents of the acyclic esters, react with dipoles generated from allenoates and PPh(3) (Lu reaction), in a completely regioselective, pi-facial selective and endo-selective manner, yielding bicyclic adducts, which are easily converted into optically pure highly substituted cyclopentane derivatives.	Cyclopentanes	369-381	caveolin 1	Homo sapiens	175-181
18651776-3	2008	The C-H BDEs for the alkenes yielding the alkyl radicals cyclopenten-4-yl and cyclohexen-4-yl and the alpha-C-H BDE in cyclopentene were also calculated.	Cyclopentanes	119-131	homeobox D13	Homo sapiens	8-11
18678486-0	2008	Structure-activity relationship study on a novel series of cyclopentane-containing macrocyclic inhibitors of the hepatitis C virus NS3/4A protease leading to the discovery of TMC435350.	Cyclopentanes	59-71	KRAS proto-oncogene, GTPase	Homo sapiens	131-134
17048264-0	2007	Long-range JCH heteronuclear coupling constants in cyclopentane derivatives.	Cyclopentanes	51-63	joining chain of multimeric IgA and IgM	Homo sapiens	11-14
17532215-0	2007	Discovery of cyclopentane- and cyclohexane-trans-1,3-diamines as potent melanin-concentrating hormone receptor 1 antagonists.	Cyclopentanes	13-25	melanin concentrating hormone receptor 1	Homo sapiens	72-112
17532215-1	2007	We herein report the optimization of cyclopentane- and cyclohexane-1,3-diamine derivatives as novel and potent MCH-R1 antagonists.	Cyclopentanes	37-49	melanin concentrating hormone receptor 1	Homo sapiens	111-117
17249732-7	2007	X-ray crystal structures of 23.2.5MeOH, 23.1.5MeCN, 24.CH2Cl2, and 24.1.5CH2Cl2 show the saddle-shape folding (typical of ex-TTF derivatives), which in 24 is enhanced by the pentamethylene chain bridging the dithiole units.	Cyclopentanes	174-188	ras homolog family member H	Homo sapiens	125-128
17305576-11	2007	Selectivity profiles and affinities depend strongly on the length of the alkylene-spacer: For some dimeric inhibitors the norepinephrine transporter (NET) and the dopamine transporter (DAT) affinities changed gradually, but for the serotonin transporter (SERT) a pentamethylene spacer showed the highest potency.	Cyclopentanes	263-277	solute carrier family 6 member 3	Homo sapiens	163-183
17305576-11	2007	Selectivity profiles and affinities depend strongly on the length of the alkylene-spacer: For some dimeric inhibitors the norepinephrine transporter (NET) and the dopamine transporter (DAT) affinities changed gradually, but for the serotonin transporter (SERT) a pentamethylene spacer showed the highest potency.	Cyclopentanes	263-277	solute carrier family 6 member 3	Homo sapiens	185-188
18671867-4	2008	RESULTS: Our search for endogenous chemical activators utilizing a bioactive lipid library screen identified a cyclopentane PGD2 metabolite, 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2), as a TRPA1 agonist.	Cyclopentanes	111-123	prostaglandin D2 synthase (brain)	Mus musculus	124-128
18671867-4	2008	RESULTS: Our search for endogenous chemical activators utilizing a bioactive lipid library screen identified a cyclopentane PGD2 metabolite, 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2), as a TRPA1 agonist.	Cyclopentanes	111-123	transient receptor potential cation channel, subfamily A, member 1	Mus musculus	195-200
17845856-0	2007	Novel potent macrocyclic inhibitors of the hepatitis C virus NS3 protease: use of cyclopentane and cyclopentene P2-motifs.	Cyclopentanes	82-94	KRAS proto-oncogene, GTPase	Homo sapiens	61-64
17845856-0	2007	Novel potent macrocyclic inhibitors of the hepatitis C virus NS3 protease: use of cyclopentane and cyclopentene P2-motifs.	Cyclopentanes	99-111	KRAS proto-oncogene, GTPase	Homo sapiens	61-64
17845856-1	2007	Several highly potent novel HCV NS3 protease inhibitors have been developed from two inhibitor series containing either a P2 trisubstituted macrocyclic cyclopentane- or a P2 cyclopentene dicarboxylic acid moiety as surrogates for the widely used N-acyl-(4R)-hydroxyproline in the P2 position.	Cyclopentanes	152-164	KRAS proto-oncogene, GTPase	Homo sapiens	32-35
17918836-1	2007	Hydroformylation of cyclopentene using Rh4(CO)12 and HRe(CO)5 as precursors.	Cyclopentanes	20-32	Rh blood group D antigen	Homo sapiens	39-42
17804225-1	2007	A successful design of conformationally restricted novel quinazolinone derivatives linked via a cyclopentene moiety as potent poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors has been developed.	Cyclopentanes	96-108	poly(ADP-ribose) polymerase 1	Homo sapiens	126-154
17804225-1	2007	A successful design of conformationally restricted novel quinazolinone derivatives linked via a cyclopentene moiety as potent poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors has been developed.	Cyclopentanes	96-108	poly(ADP-ribose) polymerase 1	Homo sapiens	156-162
16824752-0	2006	Cyclopentane-based human NK1 antagonists.	Cyclopentanes	0-12	tachykinin receptor 1	Homo sapiens	25-28
17155577-1	2006	Electron stimulated desorption of cyclopentene from the Si(100)-(2 x 1) surface is studied experimentally with cryogenic UHV STM and theoretically with transport, electronic structure, and dynamical calculations.	Cyclopentanes	34-46	sulfotransferase family 1A member 3	Homo sapiens	125-128
16958533-0	2006	Stereoselective preparation of a cyclopentane-based NK1 receptor antagonist bearing an unsymmetrically substituted sec-sec ether.	Cyclopentanes	33-45	tachykinin receptor 1	Homo sapiens	52-64
16824752-2	2006	An initial investigation of the novel cyclopentane scaffold 6 afforded low nanomolar human NK1 antagonists having enhanced water solubility properties compared to morpholine 1.	Cyclopentanes	38-50	tachykinin receptor 1	Homo sapiens	91-94
16831551-0	2006	Cyclopentane-based human NK1 antagonists.	Cyclopentanes	0-12	beta-1,3-glucuronyltransferase 1	Homo sapiens	25-28
16831551-2	2006	The synthesis and optimization of a cyclopentane-based hNK1 antagonist scaffold 3, having four chiral centers, will be discussed in the context of its enhanced water solubility properties relative to the marketed anti-emetic hNK1 antagonist EMEND (Aprepitant).	Cyclopentanes	36-48	beta-1,3-glucuronyltransferase 1	Homo sapiens	55-59
16831551-2	2006	The synthesis and optimization of a cyclopentane-based hNK1 antagonist scaffold 3, having four chiral centers, will be discussed in the context of its enhanced water solubility properties relative to the marketed anti-emetic hNK1 antagonist EMEND (Aprepitant).	Cyclopentanes	36-48	beta-1,3-glucuronyltransferase 1	Homo sapiens	225-229
16620100-2	2006	Cyclopropyl phenyl ketone underwent oxidative addition to Ni(PCy3) generated from Ni(cod)2 and PCy3 to give a nickeladihydropyran, which is a key intermediate for the Ni(0)-catalyzed homo- or heterocycloaddition to give cyclopentane compounds having two carbonyl substituents at the 1,3-position.	Cyclopentanes	220-232	COD2	Homo sapiens	82-90
16246558-1	2006	A previously discovered DHODH inhibitor series was further improved by replacing the cyclopentene ring by aromatic heterocycles.	Cyclopentanes	85-97	dihydroorotate dehydrogenase (quinone)	Homo sapiens	24-29
16475787-6	2006	Consequently, the bound BMP and PGD(2) direct their opposite faces of the cyclopentane moieties toward the nicotinamide ring of the bound NADP.	Cyclopentanes	74-86	bone morphogenetic protein 1	Homo sapiens	24-27
16161171-2	2005	This reaction, catalyzed by [Pd(dba)2] (dba=dibenzylideneacetone) in acetic acid, results in the formation of cyclopentene derivatives and [n.3.0]bicyclic systems (n=3, 4) in good to high yields.	Cyclopentanes	110-122	DBA2	Homo sapiens	32-37
16143532-1	2005	Novel DHODH inhibitors were developed based on a previously described series by introduction of heteroatoms into the cyclopentene ring and hydroxyl groups attached to it.	Cyclopentanes	117-129	dihydroorotate dehydrogenase (quinone)	Homo sapiens	6-11
16833273-1	2005	Diene-dienophile competing Diels-Alder reaction pathways of cyclopentadiene, 1H-, 2H- and 3H-phospholes with butadiene were explored at the B3LYP level using 6-31G(d) and 6-311+G(d,p) basis sets, and at the CCSD(T)/6-31G(d)//B3LYP/6-31G(d) level.	Cyclopentanes	60-75	SH2 domain containing 1A	Homo sapiens	142-145
14998586-3	2004	These compounds incorporate a valid pharmacophore for aldose reductase inhibitory activity represented by a thienocinnolinone template linked through a pentamethylene spacer to a carboxylic function.	Cyclopentanes	152-166	aldo-keto reductase family 1 member B	Homo sapiens	54-70
16104729-0	2005	Ruthenium-catalyzed cycloisomerization of cis-3-en-1-ynes to cyclopentadiene and related derivatives through a 1,5-sigmatropic hydrogen shift of ruthenium-vinylidene intermediates.	Cyclopentanes	61-76	suppressor of cytokine signaling 3	Homo sapiens	42-47
16104729-1	2005	We report a new ruthenium-catalyzed cycloisomerization of unactivated cis-3-en-1-ynes, which produces substituted cyclopentadiene and related derivatives.	Cyclopentanes	114-129	suppressor of cytokine signaling 3	Homo sapiens	70-75
12930146-2	2003	Potent and specific MMP-2, -3, -9, -13 inhibitors were obtained by regio- and stereoselective substitutions at positions 2 and 5 on the cyclopentane ring.	Cyclopentanes	136-148	matrix metallopeptidase 2	Mus musculus	20-33
12974653-1	2003	Allenes with a nucleophilic functionality connected to the alpha-carbon atom have been shown to be versatile building blocks for the syn-thesis of gamma-butenolides, gamma-lactams, gamma-iminolactones, vinylic epoxides, 4-amino-2-alkenols, 2-amino-3-alkenols, 2,5-dihydrofurans, furans, vinylic cyclopropanes, and cyclopentenes, depending on the nature of the nucleophilic centers.	Cyclopentanes	314-327	synemin	Homo sapiens	133-136
12815164-3	2003	These molecules are characterized by the presence of a reactive alpha,beta-unsatured carbonyl group in the cyclopentane ring (cyclopentenone) which is the key structure for triggering HSF1 activation.	Cyclopentanes	107-119	heat shock transcription factor 1	Homo sapiens	184-188
12371859-1	2002	The photochemical denitrogenation of the cyclopentene-annelated DBH-type azoalkanes 1 has been examined in solution as a function of bridgehead substitution and temperature.	Cyclopentanes	41-53	dopamine beta-hydroxylase	Homo sapiens	64-67
12620660-1	2003	Several heteroaromatic analogues of (2-aryl-1-cyclopentenyl-1-alkylidene)-(arylmethyloxy)amine COX-2 inhibitors, in which the cyclopentene moiety was replaced by pyrazole, thiophene or isoxazole ring, were synthesized, in order to verify the influence of the different nature of the central core on the COX inhibitory properties of these kinds of molecules.	Cyclopentanes	126-138	mitochondrially encoded cytochrome c oxidase II	Homo sapiens	95-100
12014441-3	2002	Feeding experiments with [1-13C]- and [6-13C]-D-glucose revealed that the carbon skeletons of both a glucose residue and a cyclopentane ring moiety in 1 were each derived from glucose, and that C-C bond formation between C-1 and C-5 of glucose occurred during the cyclopentane ring formation.	Cyclopentanes	264-276	heterogeneous nuclear ribonucleoprotein C	Homo sapiens	221-232
12057661-4	2002	In these substrates the fused cyclopropane moiety constrains the cyclopentane ring to mimic the conformation of a furanose sugar in the North hemisphere of the pseudorotational cycle, which matches the conformation of the ribose ring of adenosine in complex with ADA.	Cyclopentanes	65-77	adenosine deaminase	Homo sapiens	263-266
11677234-2	2002	Prostaglandin synthesis by cyclooxygenases-1 and -2 (COX-1 and COX-2) involves an initial oxygenation of arachidonic acid at C-11, followed by endoperoxide and cyclopentane ring formation, and then a second reaction with molecular oxygen in the S configuration at C-15.	Cyclopentanes	160-172	prostaglandin-endoperoxide synthase 2	Homo sapiens	27-51
11677234-2	2002	Prostaglandin synthesis by cyclooxygenases-1 and -2 (COX-1 and COX-2) involves an initial oxygenation of arachidonic acid at C-11, followed by endoperoxide and cyclopentane ring formation, and then a second reaction with molecular oxygen in the S configuration at C-15.	Cyclopentanes	160-172	mitochondrially encoded cytochrome c oxidase I	Homo sapiens	53-58
11677234-2	2002	Prostaglandin synthesis by cyclooxygenases-1 and -2 (COX-1 and COX-2) involves an initial oxygenation of arachidonic acid at C-11, followed by endoperoxide and cyclopentane ring formation, and then a second reaction with molecular oxygen in the S configuration at C-15.	Cyclopentanes	160-172	mitochondrially encoded cytochrome c oxidase II	Homo sapiens	63-68
11334571-3	2001	In this series, the bivalent ligand 16, comprised of two (+)-trans-piperidine units linked by a pentamethylene spacer, exhibits a combination of high DA transporter (DAT) and 5-HT transporter (SERT) activity (K(i) = 39 nM and 7 nM, respectively).	Cyclopentanes	96-110	solute carrier family 6 member 4	Rattus norvegicus	193-197
11728184-3	2001	This led us to design potential neuraminidase inhibitors in which the cyclopentane ring served as a scaffold for substituents (carboxylate, guanidino, acetamido, alkyl) that would interact with the four binding pockets of the neuraminidase active site at least as effectively as those of the established six-membered ring inhibitors such as DANA (2), zanamivir (3), and oseltamivir (4).	Cyclopentanes	70-82	neuraminidase 1	Homo sapiens	32-45
11728184-3	2001	This led us to design potential neuraminidase inhibitors in which the cyclopentane ring served as a scaffold for substituents (carboxylate, guanidino, acetamido, alkyl) that would interact with the four binding pockets of the neuraminidase active site at least as effectively as those of the established six-membered ring inhibitors such as DANA (2), zanamivir (3), and oseltamivir (4).	Cyclopentanes	70-82	neuraminidase 1	Homo sapiens	226-239
11348117-4	2001	On the other hand, feeding experiments with [5-(2)H]- and [6,6-(2)H(2)]-D-glucosamine showed that deuterium on C-5 and one of the two deuterium atoms on C-6 of glucosamine were lost during the cyclopentane ring formation of 1.	Cyclopentanes	193-205	complement C5	Homo sapiens	111-114
11348117-4	2001	On the other hand, feeding experiments with [5-(2)H]- and [6,6-(2)H(2)]-D-glucosamine showed that deuterium on C-5 and one of the two deuterium atoms on C-6 of glucosamine were lost during the cyclopentane ring formation of 1.	Cyclopentanes	193-205	complement C6	Homo sapiens	153-156
11348117-6	2001	These results suggested that an intermediate with a 6-aldehyde group is involved in the biosynthesis of the cyclopentane ring moiety of 1 and overall inversion of stereochemistry of the C-6 methylene group occurred by stereospecific oxidation and reduction on C-6 during the formation of 1.	Cyclopentanes	108-120	complement C6	Homo sapiens	186-189
11348117-6	2001	These results suggested that an intermediate with a 6-aldehyde group is involved in the biosynthesis of the cyclopentane ring moiety of 1 and overall inversion of stereochemistry of the C-6 methylene group occurred by stereospecific oxidation and reduction on C-6 during the formation of 1.	Cyclopentanes	108-120	complement C6	Homo sapiens	260-263
11348117-7	2001	The 6-aldehyde intermediate may play a key role in the biosynthetic step(s) of cyclization to form the cyclopentane ring and/or deoxygenation at C-5.	Cyclopentanes	103-115	complement C5	Homo sapiens	145-148
10579835-1	1999	Several cyclopentene GABA analogues were synthesized as conformationally rigid analogues of the epilepsy drug vigabatrin and tested as inhibitors and substrates of gamma-aminobutyric acid aminotransferase (GABA-AT).	Cyclopentanes	8-20	4-aminobutyrate aminotransferase	Homo sapiens	164-204
11301410-1	2001	The cyclopentenone prostaglandins PGA2, PGA1, and PGJ2 are formed by dehydration within the cyclopentane ring of PGE2, PGE1, and PGD2.	Cyclopentanes	92-104	prostaglandin D2 synthase	Homo sapiens	129-133
11457063-8	2001	The carbonyl precursors [MCp(2)(CO)] each react with perfluoro-iso-propyl iodide without loss of CO, to afford the exo-fluoroalkylated cyclopentadiene M(II) complexes MCp(eta(4)-C(5)H(5)R(F))(CO)I (21, M = Mo; 22, M = W); the exo-stereochemistry for the fluoroalkyl group is confirmed by an X-ray structural study of 22.	Cyclopentanes	135-150	CD46 molecule	Homo sapiens	25-28
11457063-8	2001	The carbonyl precursors [MCp(2)(CO)] each react with perfluoro-iso-propyl iodide without loss of CO, to afford the exo-fluoroalkylated cyclopentadiene M(II) complexes MCp(eta(4)-C(5)H(5)R(F))(CO)I (21, M = Mo; 22, M = W); the exo-stereochemistry for the fluoroalkyl group is confirmed by an X-ray structural study of 22.	Cyclopentanes	135-150	CD46 molecule	Homo sapiens	167-170
11178835-2	2001	The [4 + 4]-photocycloaddition with cyclopentadiene (CpH) proceeded smoothly and with high enantioselectivity (84-87% ee).	Cyclopentanes	36-51	carboxypeptidase E	Homo sapiens	53-56
10866624-4	2000	Studies on a series of mono, di-, and trisubstituted cyclopentenes are reported in which trans-vicinal-additions favor a syn-selective approach of electrophiles to the cyclopentene system.	Cyclopentanes	53-65	synemin	Homo sapiens	121-124
11563046-4	2001	Conformational constraints were built into the ribose rings of nucleoside and nucleotide ligands using the methanocarba approach, i.e. fused cyclopropane and cyclopentane rings in place of ribose, suggesting a preference for the Northern (N) conformation among ligands for P2Y1 and A1 and A3ARs.	Cyclopentanes	158-170	purinergic receptor P2Y1	Homo sapiens	273-294
10999251-1	2000	The synthesis of carbocyclic nucleosides, cis-9-[4-(1,2-dihydroxyethyl)-cyclopent-2-enyl]guanine (3) and cis-2-amino-6-cyclopropylamino-9-[4-(1,2-dihydroxyethyl)- cyclopent-2- enyl]purine (4), was achieved from cyclopentadiene (5) in five and six steps, respectively.	Cyclopentanes	211-226	suppressor of cytokine signaling 2	Homo sapiens	105-110
10824147-8	2000	The doubly charged Lewis acid, [CyRu(eta2-(R, R)-Ph2PCHMeCHMe Ph2PO-P,O)(solvate)]2+ derived from the chloro complex by chloride abstraction with AgSbF6 gave modest ee"s (30%) in the Diels-Alder reaction of methacrolein with cyclopentadiene.	Cyclopentanes	225-240	DNA polymerase iota	Homo sapiens	37-41
10794688-0	2000	New proline mimetics: synthesis of thrombin inhibitors incorporating cyclopentane- and cyclopentenedicarboxylic acid templates in the P2 position.	Cyclopentanes	69-81	coagulation factor II, thrombin	Homo sapiens	35-43
10579835-1	1999	Several cyclopentene GABA analogues were synthesized as conformationally rigid analogues of the epilepsy drug vigabatrin and tested as inhibitors and substrates of gamma-aminobutyric acid aminotransferase (GABA-AT).	Cyclopentanes	8-20	4-aminobutyrate aminotransferase	Homo sapiens	206-213
11674564-4	1999	All the cycloadditions occurred exclusively on the pi-face syn to the etheno bridge of 2, thereby in cases of the cycloadditions with anthracene, cyclopentadiene, 1,3-cyclohexadiene, and 6,6-dimethylfulvene producing the corresponding adducts 11a, 18b, 22b, and 23b that contain three double bonds aligned in parallel.	Cyclopentanes	146-161	synemin	Homo sapiens	59-62
11674752-1	1999	The Pauson-Khand reaction on suitable 4-oxa-hept-1-en-6-ynes (1, 17) obtained from 3,4,6-tri-O-acetyl-D-glucal gives the cyclopentane-annulated pyranosides (2, 18) that can be efficiently and stereoselectivelly transformed into chiral, advanced, highly oxygenated intermediates (10, 16, 24) for the synthesis of iridoid aglycones.	Cyclopentanes	121-133	selenoprotein I	Homo sapiens	44-50
10514291-8	1999	The configuration of the cyclopentane unit determined the affinity profile: a 1R configuration, as in (+)-3 and (-)-4, conferred higher affinity at alpha(1)-adrenoreceptors, whereas a 1S configuration, as in (-)-3 and (+)-4, produced higher affinity for 5-HT(1A) receptors.	Cyclopentanes	25-37	5-hydroxytryptamine receptor 1A	Homo sapiens	254-261
10629869-12	1999	This result indicates that this domain of the PGD receptor is responsible for distinction of structural differences between PGD2 and PGE2 on the cyclopentane ring.	Cyclopentanes	145-157	prostaglandin D receptor	Mus musculus	46-58
10629869-12	1999	This result indicates that this domain of the PGD receptor is responsible for distinction of structural differences between PGD2 and PGE2 on the cyclopentane ring.	Cyclopentanes	145-157	prostaglandin D2 synthase (brain)	Mus musculus	124-128
30382247-1	1996	Lewis acid promoted Diels-Alder reaction of acrylate esters of cis-1-arylsulfonamido-2-indanols and cyclopentadiene provided exclusively endo-adducts with high endo-diastereoselectivities.	Cyclopentanes	100-115	suppressor of cytokine signaling 1	Homo sapiens	63-68
11674049-2	1998	The ranges of activation energies for syn addition are large relative to those for anti addition, which are all similar to the activation energy for cyclopentadiene itself.	Cyclopentanes	149-164	synemin	Homo sapiens	38-41
11674049-4	1998	Deformation of the 5-fluoro-, 5-hydroxy-, and 5-amino-1,3-cyclopentadienes into their syn transition state geometries is predicted to require less energy than deformation of cyclopentadiene itself, which is in accord with experimental observation of syn addition with these dienes.	Cyclopentanes	58-73	synemin	Homo sapiens	86-89
11674049-4	1998	Deformation of the 5-fluoro-, 5-hydroxy-, and 5-amino-1,3-cyclopentadienes into their syn transition state geometries is predicted to require less energy than deformation of cyclopentadiene itself, which is in accord with experimental observation of syn addition with these dienes.	Cyclopentanes	58-73	synemin	Homo sapiens	250-253
8978850-10	1996	The effect of making the analogs more rigid by making the three-carbon chain part of a five-membered ring, but with retention of the methylene replacement for the carboxamide moiety, led to potent PKC inhibitors including anti-substituted pyrrolidine analog 35b and the most potent PKC inhibitor in the series, anti-substituted cyclopentane analog 29b.	Cyclopentanes	328-340	proline rich transmembrane protein 2	Homo sapiens	197-200
8943275-2	1996	Cyclopentenone prostaglandins, which contain an alpha, beta-unsaturated carbonyl group in the cyclopentane ring and possess antiviral activity against several RNA and DNA viruses, were shown to function as signal for HSP synthesis in a nonstressful situation in a variety of mammalian cells.	Cyclopentanes	94-106	heat shock protein family A (Hsp70) member 4	Homo sapiens	217-220
6561966-1	1984	Queuine (the base of queuosine, Q) catalytically reduced with tritium or deuterium yields a derivative in which the proton at C-8 (purine numbering system) has been exchanged and the cyclopentene ring has been reduced to a cyclopentane ring.	Cyclopentanes	183-195	homeobox C8	Homo sapiens	126-129
8841600-1	1995	Dimethyl c-4-aminomethylcyclo-pent-2-en-r-1-ylmalonate, an precursor of carbocyclic homo-nucleosides, has been synthesized from the bicyclo-[2.2.1]helpt-5-ene derivative prepared by the Diels-Alder reaction of cyclopentadiene with dimethyl trifluoroacetylaminomethylenemalonate, which is a new dienophile.	Cyclopentanes	210-225	complement C4A (Rodgers blood group)	Homo sapiens	9-12
34695350-2	2021	In the presence of a palladium catalyst, the reaction of various 1,n-dienes and diborons were converted into cyclopentane derivatives with two boryl groups at remote positions via facile regioselective transformation of an unactivated sp3 C-H bond to a C-B bond.	Cyclopentanes	109-121	Sp3 transcription factor	Homo sapiens	235-238
34257463-0	2021	Pure hydrocarbon cycles in TMC-1: Discovery of ethynyl cyclopropenylidene, cyclopentadiene and indene.	Cyclopentanes	75-90	transmembrane channel like 1	Homo sapiens	27-32
34257463-1	2021	We report the detection for the first time in space of three new pure hydrocarbon cycles in TMC-1: c-C3HCCH (ethynyl cyclopropenylidene), c-C5H6 (cyclopentadiene) and c-C9H8 (indene).	Cyclopentanes	146-161	transmembrane channel like 1	Homo sapiens	92-97
11666983-0	1996	Ab Initio Study of Endo/Exo and Diastereofacial Selectivities in Diels-Alder Reactions between Chiral Butenolides and Cyclopentadiene.	Cyclopentanes	118-133	mannosidase endo-alpha	Homo sapiens	19-23
34743520-1	2021	The flavoprotein monooxygenase (FPMO) TerC is encoded by all known cyclopentene biosynthetic gene clusters.	Cyclopentanes	67-79	telomerase RNA component	Homo sapiens	38-42
34672549-3	2021	To stabilize the electron-deficient boron atom, a series of chloroborane masked borenium ions featuring the symmetrical (B-Cl-B)+ linkage are prepared and utilized as the catalyst for the enantioselective Diels-Alder cycloaddition of cyclopentadiene and 2,2,2-trifluoroethyl acrylate.	Cyclopentanes	234-249	citramalyl-CoA lyase	Homo sapiens	123-127
34110819-0	2021	Additivity of Diene Substituent Gibbs Free Energy Contributions for Diels-Alder Reactions between (F3C)2B = NMe2 and Substituted Cyclopentadienes.	Cyclopentanes	129-145	NME/NM23 nucleoside diphosphate kinase 2	Homo sapiens	108-112
6561966-1	1984	Queuine (the base of queuosine, Q) catalytically reduced with tritium or deuterium yields a derivative in which the proton at C-8 (purine numbering system) has been exchanged and the cyclopentene ring has been reduced to a cyclopentane ring.	Cyclopentanes	223-235	homeobox C8	Homo sapiens	126-129
7111361-1	1982	Part 7: Synthesis and biological activity of some new cyclopentadienones and cyclopentadienes.	Cyclopentanes	77-93	poly(ADP-ribose) polymerase family member 15	Homo sapiens	0-6
4404464-0	1972	Utilization of a cyclopentane analog of glutamate (cis-1-amino-1,3-dicarboxycyclopentane) by glutamine synthetase.	Cyclopentanes	17-29	suppressor of cytokine signaling 1	Homo sapiens	51-56
4404464-0	1972	Utilization of a cyclopentane analog of glutamate (cis-1-amino-1,3-dicarboxycyclopentane) by glutamine synthetase.	Cyclopentanes	17-29	glutamate-ammonia ligase	Homo sapiens	93-113
33120078-3	2020	Constraining the linear propylene linker of structure I into a cyclopentene ring (II) offered improved PK parameters, while maintaining potency for PARP1.	Cyclopentanes	63-75	poly(ADP-ribose) polymerase 1	Homo sapiens	148-153
33395292-8	2021	Other typical fragment-ions produced from protonated metallocenes included the M(cp)1+ ions (M = Fe or Ni), by elimination of a cyclopentadiene molecule, or the molecular cation, by loss of a H  radical.	Cyclopentanes	128-143	C-C motif chemokine ligand 2	Homo sapiens	79-85
31549121-3	2019	We report the use of a new multifunctional cyclopentadiene (Cp) platform to prepare difunctional and monofunctional, PSMA-targeting rhenium and technetium-99m complexes.	Cyclopentanes	43-58	folate hydrolase 1	Homo sapiens	117-121
33205950-3	2020	This process is highly selective and is accompanied by the disruption of the organometallic scaffold: cyclopentadiene (CpH) and lepidocrocite (gamma-FeO(OH)) were identified by NMR and Raman analyses at the end of one representative reaction.	Cyclopentanes	102-117	carboxypeptidase E	Homo sapiens	119-122
31578059-3	2019	This route efficiently forms the cyclopentane ring from simple and easily accessible starting materials, and rapidly installs the C1/C4/C5 polar functional groups.	Cyclopentanes	33-45	heterogeneous nuclear ribonucleoprotein C	Homo sapiens	130-138
31859505-2	2020	The method relied on LiHMDS-mediated intramolecular cyclization of trisubstitued cyclopentane carboxylates bearing a leaving group (at the C-4 position) and an additional substituent (at the C-3 atom), in turn synthesized from cyclopent-3-ene carboxylate.	Cyclopentanes	81-106	complement C4A (Rodgers blood group)	Homo sapiens	139-142
31859505-2	2020	The method relied on LiHMDS-mediated intramolecular cyclization of trisubstitued cyclopentane carboxylates bearing a leaving group (at the C-4 position) and an additional substituent (at the C-3 atom), in turn synthesized from cyclopent-3-ene carboxylate.	Cyclopentanes	81-106	complement C3	Homo sapiens	191-194
31702146-1	2019	An efficient method for highly diastereoselective synthesis of chiral quaternary center-containing cyclopentenes via cinchona alkaloid derived thiosquaramide VIII catalyzed tandem Michael/Henry reaction of phenacylmalononitriles and nitroolefins.	Cyclopentanes	99-112	cytochrome c oxidase subunit 8A	Homo sapiens	158-162
31541992-4	2019	CF3 as a substituent on the 1,3,4-oxadiazole decreases the activation barriers of the rate-determining step, while CO2Me on the oxadiazole increases the activation barriers of the rate-determining step, markedly in the case of the reaction with cyclopentene and only marginally in the reactions with ethylene.	Cyclopentanes	245-257	complement C2	Homo sapiens	115-118
29518333-1	2018	G-4 calculations are used to explore which carbon atoms of methylated butadienes, methylated cyclopentadienes, and methylated benzenes are most readily protonated to yield delocalized allyl and pentadienyl cations.	Cyclopentanes	93-109	chromosome 6 open reading frame 47	Homo sapiens	0-3
31140808-1	2019	The microscopic insight into the endo/exo stereoselectivity of the Diels-Alder (DA) reaction between cyclopentadiene and methyl vinyl ketone (MVK) has posed a challenge to the computational chemists, which requires an accurate free-energy (FE) landscape.	Cyclopentanes	101-116	mannosidase endo-alpha	Homo sapiens	33-37
30873839-1	2019	We describe a stereoselective method for obtaining multigram quantities of molecular basket 1 syn in overall 11% yield, using inexpensive cyclopentadiene and diethyl fumarate as starting materials.	Cyclopentanes	138-153	synemin	Homo sapiens	94-97