Structure of PDB 6cyc Chain A Binding Site BS02

Receptor Information
>6cyc Chain A (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLYKKAGFYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSML
QDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYK
NLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEG
SVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHH
LRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIA
ELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKL
LQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL
Ligand information
Ligand IDFKJ
InChIInChI=1S/C15H13F3N4O3/c1-7(8-2-4-9(5-3-8)15(16,17)18)22-12-11(10(6-23)21-22)13(24)20-14(25)19-12/h2-5,7,23H,6H2,1H3,(H2,19,20,24,25)/t7-/m0/s1
InChIKeyJEDQNPRRXOGFJA-ZETCQYMHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c2(nn(C(c1ccc(C(F)(F)F)cc1)C)c3c2C(=O)NC(N3)=O)CO
CACTVS 3.385C[CH](n1nc(CO)c2C(=O)NC(=O)Nc12)c3ccc(cc3)C(F)(F)F
OpenEye OEToolkits 2.0.6CC(c1ccc(cc1)C(F)(F)F)n2c3c(c(n2)CO)C(=O)NC(=O)N3
CACTVS 3.385C[C@H](n1nc(CO)c2C(=O)NC(=O)Nc12)c3ccc(cc3)C(F)(F)F
OpenEye OEToolkits 2.0.6C[C@@H](c1ccc(cc1)C(F)(F)F)n2c3c(c(n2)CO)C(=O)NC(=O)N3
FormulaC15 H13 F3 N4 O3
Name3-(hydroxymethyl)-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione
ChEMBLCHEMBL4205666
DrugBank
ZINC
PDB chain6cyc 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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PDB6cyc Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor.
Resolution1.54 Å
Binding residue
(original residue number in PDB)		Y655 H656 L770 T805 D808 L809 Q812 I826 Q859 F862
Binding residue
(residue number reindexed from 1)		Y82 H83 L197 T232 D235 L236 Q239 I253 Q286 F289
Annotation score1
Binding affinityMOAD: ic50=14nM
PDBbind-CN: -logKd/Ki=7.85,IC50=14nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6cyc, PDBe:6cyc, PDBj:6cyc
PDBsum6cyc
PubMed30128073
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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