PMID-sentid	Pub_year	Sent_text		comp_official_name	comp_offsetprotein_name	organism	prot_offset
20919747-8	2010	A putative binding model was proposed based on CoMFA and CoMSIA contour maps and docking simulations; formation of pi-stacking, water bridge and specific hydrogen bonding were deemed important interactions between ligands and PDE-5.	Water	128-133	phosphodiesterase 5A	Homo sapiens	226-231	
33947926-12	2021	Considering that they are pharmaceutically active and resistant to treatment processes within an STP, it is advised that a regular monitoring and management program for PDE-5i should be developed to prevent the discharge of the pharmaceuticals into the water environment.	Water	253-258	phosphodiesterase 5A	Homo sapiens	169-174	
30394213-10	2019	While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed.	Water	20-25	phosphodiesterase 5A	Homo sapiens	90-109	
29743519-7	2018	The water-in-oil NEs can be a promising non-invasive medication for ED patients with low response to a phosphodiesterase type 5 (PDE5) inhibitor, thus increasing quality of life in the aging society.	Water	4-9	phosphodiesterase 5A	Homo sapiens	103-127	
29743519-7	2018	The water-in-oil NEs can be a promising non-invasive medication for ED patients with low response to a phosphodiesterase type 5 (PDE5) inhibitor, thus increasing quality of life in the aging society.	Water	4-9	phosphodiesterase 5A	Homo sapiens	129-133	
26846459-2	2016	PDE5 inhibitors were extracted from the samples using a 50:50 (v/v) mixture of acetonitrile and water and centrifuged.	Water	96-101	phosphodiesterase 5A	Homo sapiens	0-4	
16281046-2	2006	In co-crystals with PDE5, one of the rings of vardenafil or sildenafil interacts with Tyr(612), a catalytic site AA, via (1) a hydrogen bond with a water molecule and (2) hydrophobic bonds.	Water	148-153	phosphodiesterase 5A	Homo sapiens	20-24	
18161687-2	2008	The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO- or H2O.	Water	122-125	phosphodiesterase 5A	Homo sapiens	36-40	
18161687-3	2008	It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+.	Water	163-166	phosphodiesterase 5A	Homo sapiens	54-58	
18161687-3	2008	It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+.	Water	163-166	phosphodiesterase 5A	Homo sapiens	175-179	
18161687-3	2008	It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+.	Water	186-189	phosphodiesterase 5A	Homo sapiens	54-58	
18161687-3	2008	It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+.	Water	186-189	phosphodiesterase 5A	Homo sapiens	175-179	
18161687-5	2008	The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors.	Water	15-18	phosphodiesterase 5A	Homo sapiens	4-8	
18161687-6	2008	It is interesting to note that the PDE5(BL2 = HO-) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors.	Water	66-69	phosphodiesterase 5A	Homo sapiens	35-39	
18161687-6	2008	It is interesting to note that the PDE5(BL2 = HO-) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors.	Water	66-69	phosphodiesterase 5A	Homo sapiens	55-59	
16912214-5	2006	The molecular dynamics simulations and QM/MM calculations on PDE5 demonstrate for the first time that the BL2 in PDE5 should also be HO- rather than H2O as proposed in recently published reports on the x-ray crystal structures, which serves as the nucleophile to initialize the PDE5-catalyzed hydrolysis of cGMP.	Water	149-152	phosphodiesterase 5A	Homo sapiens	113-117	
16912214-5	2006	The molecular dynamics simulations and QM/MM calculations on PDE5 demonstrate for the first time that the BL2 in PDE5 should also be HO- rather than H2O as proposed in recently published reports on the x-ray crystal structures, which serves as the nucleophile to initialize the PDE5-catalyzed hydrolysis of cGMP.	Water	149-152	phosphodiesterase 5A	Homo sapiens	113-117