Structure of PDB 3b2r Chain A Binding Site BS01

Receptor Information
>3b2r Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFT
DLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALK
AGKIQNKLTDLEILALLIAALSHDLDHRGVCHSIMEHHHFDQCLMILNSP
GNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNL
EDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDKKNKI
PSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Ligand information
Ligand IDVDN
InChIInChI=1S/C23H32N6O4S/c1-5-8-20-24-16(4)21-23(30)25-22(26-29(20)21)18-15-17(9-10-19(18)33-7-3)34(31,32)28-13-11-27(6-2)12-14-28/h9-10,15H,5-8,11-14H2,1-4H3,(H,25,26,30)
InChIKeySECKRCOLJRRGGV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCc1nc(c2n1NC(=NC2=O)c3cc(ccc3OCC)S(=O)(=O)N4CCN(CC4)CC)C
CACTVS 3.341CCCc1nc(C)c2n1NC(=NC2=O)c3cc(ccc3OCC)[S](=O)(=O)N4CCN(CC)CC4
ACDLabs 10.04O=C2N=C(Nn1c(nc(c12)C)CCC)c3cc(ccc3OCC)S(=O)(=O)N4CCN(CC)CC4
FormulaC23 H32 N6 O4 S
Name2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE;
VARDENAFIL, LEVITRA
ChEMBLCHEMBL1520
DrugBankDB00862
ZINCZINC000018324776
PDB chain3b2r Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3b2r Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		Y612 H613 C677 I680 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		Y82 H83 C131 I134 M253 Q254 F257
Annotation score1
Binding affinityBindingDB: IC50=0.890000nM,Ki=1nM
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0007165 signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3b2r, PDBe:3b2r, PDBj:3b2r
PDBsum3b2r
PubMed17959709
UniProtO76074|PDE5A_HUMAN cGMP-specific 3',5'-cyclic phosphodiesterase (Gene Name=PDE5A)

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