Structure of PDB 5vp1 Chain B Binding Site BS02

Receptor Information
>5vp1 Chain B (length=342) 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
QDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL
Ligand information
Ligand ID9GA
InChIInChI=1S/C22H22F3N7O3/c1-12-10-31-19(29-18(12)32-11-26-13(2)30-32)16(9-27-31)20(33)28-17(21(3,4)34)14-5-7-15(8-6-14)35-22(23,24)25/h5-11,17,34H,1-4H3,(H,28,33)/t17-/m0/s1
InChIKeyHXMZXPQNCNEBPD-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncn(n1)c2nc3n(cc2C)ncc3C(=O)N[C@@H](c4ccc(OC(F)(F)F)cc4)C(C)(C)O
CACTVS 3.385Cc1ncn(n1)c2nc3n(cc2C)ncc3C(=O)N[CH](c4ccc(OC(F)(F)F)cc4)C(C)(C)O
OpenEye OEToolkits 2.0.6Cc1cn2c(c(cn2)C(=O)NC(c3ccc(cc3)OC(F)(F)F)C(C)(C)O)nc1n4cnc(n4)C
OpenEye OEToolkits 2.0.6Cc1cn2c(c(cn2)C(=O)N[C@@H](c3ccc(cc3)OC(F)(F)F)C(C)(C)O)nc1n4cnc(n4)C
ACDLabs 12.01n4cn(c1c(C)cn2ncc(c2n1)C(=O)NC(c3ccc(OC(F)(F)F)cc3)C(O)(C)C)nc4C
FormulaC22 H22 F3 N7 O3
NameN-{(1S)-2-hydroxy-2-methyl-1-[4-(trifluoromethoxy)phenyl]propyl}-6-methyl-5-(3-methyl-1H-1,2,4-triazol-1-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide
ChEMBLCHEMBL5268162
DrugBank
ZINC
PDB chain5vp1 Chain B Residue 1003 [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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PDB5vp1 Discovery of a Novel Series of Pyrazolo[1,5-a]pyrimidine-Based Phosphodiesterase 2A Inhibitors Structurally Different from N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), for the Treatment of Cognitive Disorders.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		L770 H773 T805 D808 L809 I826 M847 L858 F862
Binding residue
(residue number reindexed from 1)		L196 H199 T231 D234 L235 I252 M273 L284 F288
Annotation score1
Binding affinityMOAD: ic50=0.51nM
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
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Biological Process
External links
PDB RCSB:5vp1, PDBe:5vp1, PDBj:5vp1
PDBsum5vp1
PubMed29093293
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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