Structure of PDB 4i9z Chain A Binding Site BS01

Receptor Information
>4i9z Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNL
VQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKI
QNKLTDLEILALLIAALSHDLDHRGVNNSYLAQLYCHSIMEHHHFDQCLM
ILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRK
NQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDKNK
IPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAE
Ligand information
Ligand ID5BA
InChIInChI=1S/C23H31BrN4O3/c1-5-12-31-19-7-6-16(18(29)14-28-10-8-27(4)9-11-28)13-17(19)22-25-21(15(2)3)20(24)23(30)26-22/h6-7,13,15H,5,8-12,14H2,1-4H3,(H,25,26,30)
InChIKeyWTKMCYZVMOTXKM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCOc1ccc(cc1C2=NC(=C(Br)C(=O)N2)C(C)C)C(=O)CN3CCN(C)CC3
OpenEye OEToolkits 1.7.6CCCOc1ccc(cc1C2=NC(=C(C(=O)N2)Br)C(C)C)C(=O)CN3CCN(CC3)C
ACDLabs 12.01O=C(c2ccc(OCCC)c(C1=NC(=C(Br)C(=O)N1)C(C)C)c2)CN3CCN(CC3)C
FormulaC23 H31 Br N4 O3
Name5-bromo-2-{5-[(4-methylpiperazin-1-yl)acetyl]-2-propoxyphenyl}-6-(propan-2-yl)pyrimidin-4(3H)-one
ChEMBLCHEMBL2414314
DrugBank
ZINCZINC000095921232
PDB chain4i9z Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i9z Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		Y612 A779 V782 F786 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		Y78 A238 V241 F245 M254 Q255 F258
Annotation score1
Binding affinityMOAD: ic50=18.2nM
PDBbind-CN: -logKd/Ki=7.74,IC50=18.2nM
BindingDB: IC50=18nM
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:4i9z, PDBe:4i9z, PDBj:4i9z
PDBsum4i9z
PubMed23867165
UniProtO76074|PDE5A_HUMAN cGMP-specific 3',5'-cyclic phosphodiesterase (Gene Name=PDE5A)

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