Structure of PDB 5sex Chain B Binding Site BS02

Receptor Information
>5sex Chain B (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELE
KLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGL
LIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLE
GHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNL
NNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKL
GIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACR
DNLSQWEKVIRGEET
Ligand information
Ligand IDII9
InChIInChI=1S/C22H19N5O2/c1-13-7-6-10-16(24-13)22(29)27-17-12-19-18(11-15(17)21(28)23-2)25-20(26-19)14-8-4-3-5-9-14/h3-12H,1-2H3,(H,23,28)(H,25,26)(H,27,29)
InChIKeyFEZUIXBPOZHUAQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)c1cc2nc([nH]c2cc1NC(=O)c3cccc(C)n3)c4ccccc4
OpenEye OEToolkits 2.0.7Cc1cccc(n1)C(=O)Nc2cc3c(cc2C(=O)NC)nc([nH]3)c4ccccc4
ACDLabs 12.01Cc1cccc(n1)C(=O)Nc1cc2[NH]c(nc2cc1C(=O)NC)c1ccccc1
FormulaC22 H19 N5 O2
NameN-methyl-6-[(6-methylpyridine-2-carbonyl)amino]-2-phenyl-1H-benzimidazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5sex Chain B Residue 803 [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]
PDB5sex A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		I692 Y693 P712 M713 E721 G725 F729
Binding residue
(residue number reindexed from 1)		I236 Y237 P256 M257 E265 G269 F273
Annotation score1
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:5sex, PDBe:5sex, PDBj:5sex
PDBsum5sex
PubMed36153472
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

[Back to BioLiP]