Structure of PDB 5xkm Chain B Binding Site BS02

Receptor Information
>5xkm Chain B (length=345) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHASDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQ
DMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKN
LELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGS
VMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHL
RIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAE
LIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLL
QDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
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 B 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)		T768 L770 H773 T805 L809 I826 F830 Q859 F862
Binding residue
(residue number reindexed from 1)		T194 L196 H199 T231 L235 I252 F256 Q285 F288
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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