PMID-sentid	Pub_year	Sent_text	compound_name	comp_offset	prot_official_name	organism	prot_offset
29624884-5	2018	Specifically, for CD4 binding site (CD4bs), the binding of antibodies has different effects on CD4bs with and without CD4.	cd4bs	36-41	CD4 molecule	Homo sapiens	18-21
30404804-5	2019	Env pseudotyped CRF02_AG viruses were best neutralized by the CD4 binding site (CD4bs)-directed bnAbs (VRC01, 3BNC117, NIH45-46G54W, and N6) and the gp41 membrane-proximal external region (MPER)-directed bnAb 10E8 in terms of both potency and breadth.	cd4bs	80-85	endogenous retrovirus group W member 1, envelope	Homo sapiens	0-3
30404804-5	2019	Env pseudotyped CRF02_AG viruses were best neutralized by the CD4 binding site (CD4bs)-directed bnAbs (VRC01, 3BNC117, NIH45-46G54W, and N6) and the gp41 membrane-proximal external region (MPER)-directed bnAb 10E8 in terms of both potency and breadth.	cd4bs	80-85	CD4 molecule	Homo sapiens	62-65
25253346-4	2014	Here we engineered additional N-linked glycans onto a cysteine-stabilized gp120 core (0G) deleted of its major variable regions to preferentially expose the conformationally fixed CD4bs.	cd4bs	180-185	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	74-79
29118121-7	2018	Our data indicated that the CD4 binding site (CD4bs) is highly occluded on Env trimers of non-mac-tropic R5 viruses.	cd4bs	46-51	CD4 molecule	Homo sapiens	28-31
29118121-7	2018	Our data indicated that the CD4 binding site (CD4bs) is highly occluded on Env trimers of non-mac-tropic R5 viruses.	cd4bs	46-51	endogenous retrovirus group K member 20	Homo sapiens	75-78
29020058-7	2017	Thus, pulsed exposures to DNA and MVA-expressed VLPs plus gp120 protein of a T/F Env can induce autologous tier 2 nAbs to the CD4bs.	cd4bs	126-131	endogenous retrovirus group V member 2 Env polyprotein	Macaca mulatta	81-84
28902916-4	2017	We focused on the conserved CD4 binding site (CD4bs) since this is a known neutralizing determinant that is devoid of glycosylation to allow CD4 receptor engagement, but is ringed by surrounding N-glycans.	cd4bs	46-51	T-cell surface glycoprotein CD4	Oryctolagus cuniculus	28-31
28696188-8	2017	A salient observation was the presence of CD4 binding site (CD4bs)-specific NAbs in patient #18 that improved with time (1.76-fold).	cd4bs	60-65	CD4 molecule	Homo sapiens	42-45
28696188-10	2017	Further, the presence of CD4bs-neutralizing determinants in patient #18"s plasma was confirmed by the neutralizing activity demonstrated by the CD4bs-directed IgG fraction purified from this plasma, and competition with sCD4 against JRFLgp120, identifying this paediatric donor as a potential candidate for the isolation of CD4bs-directed bnAbs.	cd4bs	25-30	stearoyl-CoA desaturase 5	Homo sapiens	220-224
28696188-10	2017	Further, the presence of CD4bs-neutralizing determinants in patient #18"s plasma was confirmed by the neutralizing activity demonstrated by the CD4bs-directed IgG fraction purified from this plasma, and competition with sCD4 against JRFLgp120, identifying this paediatric donor as a potential candidate for the isolation of CD4bs-directed bnAbs.	cd4bs	25-30	CD4 molecule	Homo sapiens	144-147
28968970-4	2017	It efficiently blocked the binding of soluble CD4 to gp120 and competed with the CD4-binding site (CD4bs)-specific mAbs.	cd4bs	99-104	CD4 molecule	Homo sapiens	46-49
28968970-4	2017	It efficiently blocked the binding of soluble CD4 to gp120 and competed with the CD4-binding site (CD4bs)-specific mAbs.	cd4bs	99-104	CD4 molecule	Homo sapiens	81-84
28332627-9	2017	This is the first study to identify cross neutralizing scFv monoclonals with CD4bs and N332 glycan specificities from India.	cd4bs	77-82	immunglobulin heavy chain variable region	Homo sapiens	55-59
24801282-6	2014	This variant retains excellent binding affinity for peptide triazoles, for sCD4 and other CD4 binding site (CD4bs) ligands, and for a CD4-induced (CD4i) ligand that binds the coreceptor recognition site.	cd4bs	108-113	stearoyl-CoA desaturase 5	Homo sapiens	75-79
24801282-6	2014	This variant retains excellent binding affinity for peptide triazoles, for sCD4 and other CD4 binding site (CD4bs) ligands, and for a CD4-induced (CD4i) ligand that binds the coreceptor recognition site.	cd4bs	108-113	CD4 molecule	Homo sapiens	76-79
24801282-6	2014	This variant retains excellent binding affinity for peptide triazoles, for sCD4 and other CD4 binding site (CD4bs) ligands, and for a CD4-induced (CD4i) ligand that binds the coreceptor recognition site.	cd4bs	108-113	CD4 molecule	Homo sapiens	90-93
24179160-3	2013	We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution.	cd4bs	174-179	endogenous retrovirus group K member 20	Homo sapiens	96-99
24884925-8	2014	Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope.	cd4bs	63-68	CD4 molecule	Homo sapiens	85-88
24179160-3	2013	We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution.	cd4bs	174-179	CD4 molecule	Homo sapiens	156-159
23843636-2	2013	A potential vaccine design strategy is to stabilize Env, thereby focusing antibody responses on constitutively exposed, conserved surfaces, such as the CD4 binding site (CD4bs).	cd4bs	170-175	CD4 molecule	Homo sapiens	152-155
22345481-9	2012	We conclude that potent CD4bs bnMAbs can display differences in the way they recognize and access the CD4bs and that mimicry of CD4, as assessed by inducing conformational changes in monomeric gp120 that lead to enhanced exposure of the CD4i site, is not uniquely correlated with effective neutralization at the site of CD4 binding on HIV-1.	cd4bs	24-29	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	193-198
22906742-5	2012	In this study, we test our hypothesis that CD4-induced (CD4i) antibodies, which target the CoRbs, could also induce conformational changes in gp120 leading to better exposed conserved neutralizing antibody epitopes including the CD4-binding site (CD4bs).	cd4bs	247-252	CD4 molecule	Homo sapiens	43-46
22906742-5	2012	In this study, we test our hypothesis that CD4-induced (CD4i) antibodies, which target the CoRbs, could also induce conformational changes in gp120 leading to better exposed conserved neutralizing antibody epitopes including the CD4-binding site (CD4bs).	cd4bs	247-252	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	142-147
22906742-5	2012	In this study, we test our hypothesis that CD4-induced (CD4i) antibodies, which target the CoRbs, could also induce conformational changes in gp120 leading to better exposed conserved neutralizing antibody epitopes including the CD4-binding site (CD4bs).	cd4bs	247-252	CD4 molecule	Homo sapiens	56-59
22551420-2	2012	The CD4 binding site (CD4bs) of gp120, and especially a recessed cavity occupied by the CD4 Phe43 residue, are known to be highly conserved among the different circulating subtypes and therefore constitute particularly interesting targets for vaccine and drug design.	cd4bs	22-27	CD4 molecule	Homo sapiens	4-7
22551420-2	2012	The CD4 binding site (CD4bs) of gp120, and especially a recessed cavity occupied by the CD4 Phe43 residue, are known to be highly conserved among the different circulating subtypes and therefore constitute particularly interesting targets for vaccine and drug design.	cd4bs	22-27	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	32-37
22345481-9	2012	We conclude that potent CD4bs bnMAbs can display differences in the way they recognize and access the CD4bs and that mimicry of CD4, as assessed by inducing conformational changes in monomeric gp120 that lead to enhanced exposure of the CD4i site, is not uniquely correlated with effective neutralization at the site of CD4 binding on HIV-1.	cd4bs	24-29	CD4 molecule	Homo sapiens	102-105
22345481-9	2012	We conclude that potent CD4bs bnMAbs can display differences in the way they recognize and access the CD4bs and that mimicry of CD4, as assessed by inducing conformational changes in monomeric gp120 that lead to enhanced exposure of the CD4i site, is not uniquely correlated with effective neutralization at the site of CD4 binding on HIV-1.	cd4bs	102-107	CD4 molecule	Homo sapiens	24-27
22345481-9	2012	We conclude that potent CD4bs bnMAbs can display differences in the way they recognize and access the CD4bs and that mimicry of CD4, as assessed by inducing conformational changes in monomeric gp120 that lead to enhanced exposure of the CD4i site, is not uniquely correlated with effective neutralization at the site of CD4 binding on HIV-1.	cd4bs	102-107	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	193-198
19879224-4	2009	The present study shows that significant increases in the antigenicity of the V3 and C1 regions of gp120 were attained for several subtype B gp120s and a subtype C gp120 upon immune complex formation with the anti-CD4bs monoclonal Ab (mAb) 654-D.	cd4bs	214-219	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	99-104
22329717-2	2012	Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones.	cd4bs	135-140	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	35-40
22329717-2	2012	Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones.	cd4bs	135-140	CD4 molecule	Homo sapiens	117-120
22496655-5	2012	While gp41 directed agents remain active, CD4 binding site (CD4bs) directed inhibitors, including the potent neutralizing mAb VRC01, dramatically lose potency during cell-cell transmission.	cd4bs	60-65	CD4 molecule	Homo sapiens	42-45
21697467-3	2011	In this study, we investigated the interaction of the lectin griffithsin (GRFT) with HIV-1 gp120 and its effects on exposure of the CD4-binding site (CD4bs).	cd4bs	150-155	CD4 molecule	Homo sapiens	132-135
21635737-9	2011	Furthermore, we now provide new evidence that these CD4bs alterations augment the ability of gp120 to interact with CD4 by increasing the exposure of the CD4bs.	cd4bs	52-57	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	93-98
21635737-9	2011	Furthermore, we now provide new evidence that these CD4bs alterations augment the ability of gp120 to interact with CD4 by increasing the exposure of the CD4bs.	cd4bs	52-57	CD4 molecule	Homo sapiens	116-119
22693444-8	2012	Both groups of Envs also exhibited the same CD4+ T cell subset tropism and showed similar sensitivity to neutralization by CD4 binding site (CD4bs) antibodies.	cd4bs	141-146	CD4 molecule	Homo sapiens	123-126
19879224-4	2009	The present study shows that significant increases in the antigenicity of the V3 and C1 regions of gp120 were attained for several subtype B gp120s and a subtype C gp120 upon immune complex formation with the anti-CD4bs monoclonal Ab (mAb) 654-D.	cd4bs	214-219	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	141-146
19146663-7	2009	Viral sequences from 4 of the 5 LTNPs showed extensive positive selective pressure on the CD4-binding site (CD4bs).	cd4bs	108-113	CD4 molecule	Homo sapiens	90-93
18519142-3	2008	The 3D structure of gp120 shows five loop structures that surround the CD4 binding site (CD4BS) and may restrict antibody access to the site.	cd4bs	89-94	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	20-25
18815292-2	2008	Adsorption with gp120 immobilized on beads revealed that an often large but variable fraction of plasma neutralization was directed to gp120 and that in some cases, neutralization was largely mediated by CD4 binding site (CD4bs) Abs.	cd4bs	222-227	CD4 molecule	Homo sapiens	204-207
18638381-5	2008	As expected, anti-CD4bs Abs were generated only after immunization with CD4bs+ Env and not with CD4bs- Env.	cd4bs	18-23	endogenous retrovirus group K member 20	Homo sapiens	79-82
18638381-5	2008	As expected, anti-CD4bs Abs were generated only after immunization with CD4bs+ Env and not with CD4bs- Env.	cd4bs	72-77	CD4 molecule	Homo sapiens	18-21
18638381-6	2008	The presence of anti-CD4bs Abs was associated with lower levels of envelope-specific lymphoproliferation in animals immunized with CD4bs+ Env.	cd4bs	21-26	endogenous retrovirus group K member 20	Homo sapiens	138-141
18237398-9	2008	Neutralization by soluble CD4 and the neutralizing CD4 binding site (CD4BS) antibody b12 was significantly enhanced in the absence of the 386 sugar, indicating that this glycan protects the CD4BS against antibodies.	cd4bs	69-74	CD4 molecule	Homo sapiens	51-54
15542540-1	2004	In an attempt to design immunogens that elicit broadly HIV-neutralizing antibodies, we recently engineered monomeric HIV-1 gp120 to bind preferentially b12, a broadly neutralizing antibody to the CD4-binding site (CD4bs) on gp120, by mutating four central residues in the CD4bs to alanine and introducing extra N-glycosylation sites potentially to mask unwanted B-cell epitopes.	cd4bs	214-219	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	123-128
15542540-1	2004	In an attempt to design immunogens that elicit broadly HIV-neutralizing antibodies, we recently engineered monomeric HIV-1 gp120 to bind preferentially b12, a broadly neutralizing antibody to the CD4-binding site (CD4bs) on gp120, by mutating four central residues in the CD4bs to alanine and introducing extra N-glycosylation sites potentially to mask unwanted B-cell epitopes.	cd4bs	214-219	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	224-229
12829845-5	2003	Additionally, the V3 loop region was found to interact functionally with sequences in the outer domain of gp120, distant from the CD4bs and coreceptor-binding site, as well as with a residue thought to be located centrally in the coreceptor-binding site.	cd4bs	130-135	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	106-111
12477840-5	2003	Nevertheless, in a more interpretable competition format, it is shown that nonneutralizing anti-CD4 binding site (CD4bs) Abs compete with a neutralizing anti-CD4bs Ab (b12) for virus capture, suggesting that the nonneutralizing anti-CD4bs Abs are able to bind to the envelope species that is involved in virion capture in these experiments.	cd4bs	114-119	CD4 molecule	Homo sapiens	96-99
12477867-1	2003	Alanine scanning mutagenesis was performed on monomeric gp120 of human immunodeficiency virus type 1 to systematically identify residues important for gp120 recognition by neutralizing and nonneutralizing monoclonal antibodies (MAbs) to the CD4 binding site (CD4bs).	cd4bs	259-264	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	151-156
18076768-4	2007	Sequence analysis identified the presence of Asn 362 (N362), a potential N-linked glycosylation site immediately N-terminal to CD4-binding site (CD4bs) residues in the C3 region of gp120, more frequently in A-R5 Envs than PA-R5 Envs.	cd4bs	145-150	CD4 molecule	Homo sapiens	127-130
18076768-4	2007	Sequence analysis identified the presence of Asn 362 (N362), a potential N-linked glycosylation site immediately N-terminal to CD4-binding site (CD4bs) residues in the C3 region of gp120, more frequently in A-R5 Envs than PA-R5 Envs.	cd4bs	145-150	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	181-186
18076768-8	2007	CONCLUSION: Enhanced fusogenicity is a phenotype of the A-R5 Envs studied, which was associated with the presence of N362, enhanced HIV-1 entry kinetics and increased CD4bs exposure in gp120.	cd4bs	167-172	Envelope surface glycoprotein gp160, precursor	Human immunodeficiency virus 1	185-190
12768015-6	2003	In sharp contrast, 4KG5 binding to gp120 is inhibited by soluble CD4 (sCD4) and by all other (n = 14) anti-CD4bs MAbs tested.	cd4bs	107-112	inter-alpha-trypsin inhibitor heavy chain 4	Homo sapiens	35-40