Structure of PDB 5seg Chain D Binding Site BS02

Receptor Information
>5seg Chain D (length=310) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKL
CRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLI
ACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGH
NIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNN
QSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGI
QPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDN
LSQWEKVIRG
Ligand information
Ligand IDIFN
InChIInChI=1S/C24H20BrN5O4/c1-30-10-14(25)7-17(24(30)33)23(32)29-18-9-20-19(8-16(18)22(31)26-15-11-34-12-15)27-21(28-20)13-5-3-2-4-6-13/h2-10,15H,11-12H2,1H3,(H,26,31)(H,27,28)(H,29,32)
InChIKeyWXPYFTHDDRZTRR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1C=C(C=C(C1=O)C(=O)Nc2cc3c(cc2C(=O)NC4COC4)[nH]c(n3)c5ccccc5)Br
ACDLabs 12.01O=C(NC1COC1)c1cc2[NH]c(nc2cc1NC(=O)C1=CC(Br)=CN(C)C1=O)c1ccccc1
CACTVS 3.385CN1C=C(Br)C=C(C(=O)Nc2cc3nc([nH]c3cc2C(=O)NC4COC4)c5ccccc5)C1=O
FormulaC24 H20 Br N5 O4
Name5-[(5-bromo-1-methyl-2-oxo-1,2-dihydropyridine-3-carbonyl)amino]-N-(oxetan-3-yl)-2-phenyl-1H-benzimidazole-6-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5seg Chain D Residue 803 [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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PDB5seg A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		L675 Y693 F696 M713 E721 G725 F729 V733
Binding residue
(residue number reindexed from 1)		L217 Y235 F238 M255 E263 G267 F271 V275
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:5seg, PDBe:5seg, PDBj:5seg
PDBsum5seg
PubMed36153472
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

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