Structure of PDB 5sdw Chain D Binding Site BS02

Receptor Information
>5sdw Chain D (length=313) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFEL
EKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKG
LLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQL
EGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLN
LNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKK
LGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKAC
RDNLSQWEKVIRG
Ligand information
Ligand IDIAL
InChIInChI=1S/C21H20N6O2/c1-26(2)21(29)15-12-22-27(3)18(15)20(28)23-14-9-10-16-17(11-14)25-19(24-16)13-7-5-4-6-8-13/h4-12H,1-3H3,(H,23,28)(H,24,25)
InChIKeyFPXYSABPAGHOSR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c1cnn(C)c1C(=O)Nc1ccc2[NH]c(nc2c1)c1ccccc1)N(C)C
OpenEye OEToolkits 2.0.7Cn1c(c(cn1)C(=O)N(C)C)C(=O)Nc2ccc3c(c2)nc([nH]3)c4ccccc4
CACTVS 3.385CN(C)C(=O)c1cnn(C)c1C(=O)Nc2ccc3[nH]c(nc3c2)c4ccccc4
FormulaC21 H20 N6 O2
NameN~4~,N~4~,1-trimethyl-N~5~-(2-phenyl-1H-benzimidazol-5-yl)-1H-pyrazole-4,5-dicarboxamide
ChEMBL
DrugBank
ZINC
PDB chain5sdw 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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PDB5sdw A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		I692 Y693 F696 M713 E721 G725 Q726 F729
Binding residue
(residue number reindexed from 1)		I237 Y238 F241 M258 E266 G270 Q271 F274
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:5sdw, PDBe:5sdw, PDBj:5sdw
PDBsum5sdw
PubMed36153472
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

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