Structure of PDB 4phw Chain A Binding Site BS02

Receptor Information
>4phw Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIM
SVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCH
DLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFST
LSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRD
RVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPM
MDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWE
KVIRG
Ligand information
Ligand ID2W1
InChIInChI=1S/C24H21N3O3/c28-22(23-26-20-5-1-2-6-21(20)27-23)17-7-9-18(10-8-17)30-24-19(4-3-13-25-24)16-11-14-29-15-12-16/h1-10,13,16H,11-12,14-15H2,(H,26,27)
InChIKeyNQQHFVCQMJVYTB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c2nc1ccccc1n2)c5ccc(Oc3ncccc3C4CCOCC4)cc5
OpenEye OEToolkits 1.9.2c1ccc2c(c1)[nH]c(n2)C(=O)c3ccc(cc3)Oc4c(cccn4)C5CCOCC5
CACTVS 3.385O=C(c1[nH]c2ccccc2n1)c3ccc(Oc4ncccc4C5CCOCC5)cc3
FormulaC24 H21 N3 O3
Name1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone
ChEMBLCHEMBL3319208
DrugBank
ZINCZINC000098208330
PDB chain4phw Chain A Residue 805 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4phw Discovery of Clinical Candidate 1-(4-(3-(4-(1H-Benzo[d]imidazole-2-carbonyl)phenoxy)pyrazin-2-yl)piperidin-1-yl)ethanone (AMG 579), A Potent, Selective, and Efficacious Inhibitor of Phosphodiesterase 10A (PDE10A).
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I682 Y683 F686 P702 M703 E711 V712 G715 F719
Binding residue
(residue number reindexed from 1)		I229 Y230 F233 P249 M250 E258 V259 G262 F266
Annotation score1
Binding affinityMOAD: ic50=0.1nM
PDBbind-CN: -logKd/Ki=10.00,IC50=0.1nM
BindingDB: IC50=0.17nM
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:4phw, PDBe:4phw, PDBj:4phw
PDBsum4phw
PubMed25062128
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

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