Structure of PDB 3ws8 Chain A Binding Site BS02

Receptor Information
>3ws8 Chain A (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHR
SCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHT
LFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHF
SQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLE
EMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEF
WAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILP
PTEPLLKACRDNLSQWEKVIRGEE
Ligand information
Ligand IDX4C
InChIInChI=1S/C23H21N5/c1-16-9-10-20-19(15-16)26-22(28(20)18-7-4-3-5-8-18)12-11-21-25-17(2)23-24-13-6-14-27(21)23/h3-10,13-15H,11-12H2,1-2H3
InChIKeyVOYXDWSUNQJWTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1ccc2c(c1)nc(n2c3ccccc3)CCc4nc(c5n4cccn5)C
CACTVS 3.385Cc1ccc2n(c(CCc3nc(C)c4ncccn34)nc2c1)c5ccccc5
ACDLabs 12.01n2c1cc(ccc1n(c2CCc4nc(c3ncccn34)C)c5ccccc5)C
FormulaC23 H21 N5
Name8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine
ChEMBLCHEMBL3288410
DrugBank
ZINCZINC000098209601
PDB chain3ws8 Chain A Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ws8 Novel benzimidazole derivatives as phosphodiesterase 10A (PDE10A) inhibitors with improved metabolic stability.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		I692 Y693 F696 M713 Q726 F729
Binding residue
(residue number reindexed from 1)		I246 Y247 F250 M267 Q280 F283
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.68,IC50=210nM
BindingDB: IC50=210nM
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:3ws8, PDBe:3ws8, PDBj:3ws8
PDBsum3ws8
PubMed24837154
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

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