Structure of PDB 6cyd Chain A Binding Site BS02

Receptor Information
>6cyd 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 IDFKG
InChIInChI=1S/C16H15F3N4O2/c1-8(10-3-5-11(6-4-10)16(17,18)19)23-14-13(12(7-24)22-23)15(25)21-9(2)20-14/h3-6,8,24H,7H2,1-2H3,(H,20,21,25)/t8-/m0/s1
InChIKeyWOPONWMJGIDXSF-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=Nc2c(c(nn2[C@@H](C)c3ccc(cc3)C(F)(F)F)CO)C(=O)N1
CACTVS 3.385C[C@H](n1nc(CO)c2C(=O)NC(=Nc12)C)c3ccc(cc3)C(F)(F)F
ACDLabs 12.01c2(nn(C(c1ccc(C(F)(F)F)cc1)C)c3c2C(=O)NC(C)=N3)CO
CACTVS 3.385C[CH](n1nc(CO)c2C(=O)NC(=Nc12)C)c3ccc(cc3)C(F)(F)F
OpenEye OEToolkits 2.0.6CC1=Nc2c(c(nn2C(C)c3ccc(cc3)C(F)(F)F)CO)C(=O)N1
FormulaC16 H15 F3 N4 O2
Name3-(hydroxymethyl)-6-methyl-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL4211122
DrugBank
ZINC
PDB chain6cyd 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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PDB6cyd Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		L770 D808 L809 Q812 I826 Q859 F862
Binding residue
(residue number reindexed from 1)		L197 D235 L236 Q239 I253 Q286 F289
Annotation score1
Binding affinityMOAD: ic50=2nM
PDBbind-CN: -logKd/Ki=8.70,IC50=2nM
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:6cyd, PDBe:6cyd, PDBj:6cyd
PDBsum6cyd
PubMed30128073
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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