Structure of PDB 3b2r Chain B Binding Site BS01

Receptor Information
>3b2r Chain B (length=287) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQN
FQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNK
LTDLEILALLIAALSHDLDHRGCHSIMEHHHFDQCLMILNSPGNQILSGL
SIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKEL
FLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQKKNKIPSMQVGFIDA
ICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
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 B 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 C677 I680 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		Y75 C123 I126 M243 Q244 F247
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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