Structure of PDB 4htx Chain A Binding Site BS02

Receptor Information
>4htx Chain A (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNF
INNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELT
NYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMER
HHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFK
DLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYK
EFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLF
PKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL
Ligand information
Ligand ID19F
InChIInChI=1S/C27H32N4O4/c1-17-25-27(33)29-24(16-20-13-14-22(34-3)23(15-20)35-4)30-31(25)26(28-17)21(18(2)32)12-8-11-19-9-6-5-7-10-19/h5-7,9-10,13-15,18,21,32H,8,11-12,16H2,1-4H3,(H,29,30,33)/t18-,21+/m1/s1
InChIKeyMYTWFJKBZGMYCS-NQIIRXRSSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1ccc(CC2=Nn3c(nc(C)c3C(=O)N2)[C@@H](CCCc4ccccc4)[C@@H](C)O)cc1OC
OpenEye OEToolkits 1.7.6Cc1c2n(c(n1)[C@@H](CCCc3ccccc3)[C@@H](C)O)N=C(NC2=O)Cc4ccc(c(c4)OC)OC
CACTVS 3.370COc1ccc(CC2=Nn3c(nc(C)c3C(=O)N2)[CH](CCCc4ccccc4)[CH](C)O)cc1OC
ACDLabs 12.01O=C1c3c(nc(n3N=C(N1)Cc2ccc(OC)c(OC)c2)C(CCCc4ccccc4)C(O)C)C
OpenEye OEToolkits 1.7.6Cc1c2n(c(n1)C(CCCc3ccccc3)C(C)O)N=C(NC2=O)Cc4ccc(c(c4)OC)OC
FormulaC27 H32 N4 O4
Name2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one;
BAY60-7550
ChEMBLCHEMBL370962
DrugBank
ZINCZINC000000596596
PDB chain4htx Chain A Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4htx X-ray Crystal Structure of Phosphodiesterase 2 in Complex with a Highly Selective, Nanomolar Inhibitor Reveals a Binding-Induced Pocket Important for Selectivity.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y655 L770 H773 L809 I826 F830 M847 L858 Q859 F862 I866
Binding residue
(residue number reindexed from 1)		Y77 L192 H195 L231 I248 F252 M269 L280 Q281 F284 I288
Annotation score1
Binding affinityMOAD: ic50=4.7nM
PDBbind-CN: -logKd/Ki=8.33,IC50=4.7nM
BindingDB: IC50=4.7nM
Enzymatic activity
Enzyme Commision number 3.1.4.17: 3',5'-cyclic-nucleotide 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:4htx, PDBe:4htx, PDBj:4htx
PDBsum4htx
PubMed23899287
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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