Structure of PDB 5xkm Chain E Binding Site BS02

Receptor Information
>5xkm Chain E (length=319) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTL
ARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFAL
FISCMCHDLDHRGTNNSFQVASSEGSVMERHHFAQAIAILNTHGCNIFDH
FSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRL
LLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMM
DREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKV
SHKFTIRGLPSNNSLDFLD
Ligand information
Ligand ID87R
InChIInChI=1S/C18H17F3N4O2/c1-3-15(12-4-6-13(7-5-12)27-18(19,20)21)24-17(26)14-9-23-25-10-11(2)8-22-16(14)25/h4-10,15H,3H2,1-2H3,(H,24,26)/t15-/m1/s1
InChIKeyCXEGBNQZVKLHTO-OAHLLOKOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[CH](NC(=O)c1cnn2cc(C)cnc12)c3ccc(OC(F)(F)F)cc3
OpenEye OEToolkits 2.0.6CCC(c1ccc(cc1)OC(F)(F)F)NC(=O)c2cnn3c2ncc(c3)C
OpenEye OEToolkits 2.0.6CC[C@H](c1ccc(cc1)OC(F)(F)F)NC(=O)c2cnn3c2ncc(c3)C
CACTVS 3.385CC[C@@H](NC(=O)c1cnn2cc(C)cnc12)c3ccc(OC(F)(F)F)cc3
FormulaC18 H17 F3 N4 O2
Name6-methyl-N-[(1R)-1-[4-(trifluoromethyloxy)phenyl]propyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
ChEMBLCHEMBL4059831
DrugBank
ZINC
PDB chain5xkm Chain E Residue 2003 [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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PDB5xkm Discovery of an Orally Bioavailable, Brain-Penetrating, in Vivo Active Phosphodiesterase 2A Inhibitor Lead Series for the Treatment of Cognitive Disorders.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		H656 T768 L770 H773 T805 D808 L809 I826 F830 F862
Binding residue
(residue number reindexed from 1)		H67 T170 L172 H175 T207 D210 L211 I228 F232 F264
Annotation score1
Binding affinityMOAD: ic50=24nM
BindingDB: IC50=53nM
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:5xkm, PDBe:5xkm, PDBj:5xkm
PDBsum5xkm
PubMed28759228
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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