Structure of PDB 5vp0 Chain A Binding Site BS02

Receptor Information
>5vp0 Chain A (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNY
KIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLE
DIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFA
QAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQK
MAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFS
QGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAA
ELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL
Ligand information
Ligand ID9GJ
InChIInChI=1S/C19H18F4N4O5/c1-30-9-14(10-3-4-15(12(20)5-10)32-19(21,22)23)26-18(29)27-8-16(28)25-13-6-11(31-2)7-24-17(13)27/h3-7,14H,8-9H2,1-2H3,(H,25,28)(H,26,29)/t14-/m1/s1
InChIKeyAWJSRXUQLSPAOI-CQSZACIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COC[C@H](c1ccc(c(c1)F)OC(F)(F)F)NC(=O)N2CC(=O)Nc3c2ncc(c3)OC
OpenEye OEToolkits 2.0.6COCC(c1ccc(c(c1)F)OC(F)(F)F)NC(=O)N2CC(=O)Nc3c2ncc(c3)OC
CACTVS 3.385COC[C@@H](NC(=O)N1CC(=O)Nc2cc(OC)cnc12)c3ccc(OC(F)(F)F)c(F)c3
ACDLabs 12.01n1cc(cc2NC(=O)CN(c12)C(NC(c3cc(c(cc3)OC(F)(F)F)F)COC)=O)OC
CACTVS 3.385COC[CH](NC(=O)N1CC(=O)Nc2cc(OC)cnc12)c3ccc(OC(F)(F)F)c(F)c3
FormulaC19 H18 F4 N4 O5
NameN-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide
ChEMBLCHEMBL4060569
DrugBank
ZINC
PDB chain5vp0 Chain A Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5vp0 Discovery of Clinical Candidate 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): A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L770 H773 T805 L809 Q812 I826 M847 Q859 F862
Binding residue
(residue number reindexed from 1)		L188 H191 T223 L227 Q230 I244 M265 Q277 F280
Annotation score1
Binding affinityMOAD: ic50=0.61nM
PDBbind-CN: -logKd/Ki=9.21,IC50=0.61nM
BindingDB: IC50=0.610000nM
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:5vp0, PDBe:5vp0, PDBj:5vp0
PDBsum5vp0
PubMed28796496
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

[Back to BioLiP]