Structure of PDB 5sfj Chain D Binding Site BS02

Receptor Information
>5sfj 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 IDIKZ
InChIInChI=1S/C24H20N8O2/c1-31-21(18(14-27-31)22(33)26-13-17-9-5-6-11-25-17)23(34)29-20-10-12-32-15-19(28-24(32)30-20)16-7-3-2-4-8-16/h2-12,14-15H,13H2,1H3,(H,26,33)(H,28,29,30,34)
InChIKeyRWQPESJHMNDXMR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cn1c(c(cn1)C(=O)NCc2ccccn2)C(=O)Nc3ccn4cc(nc4n3)c5ccccc5
CACTVS 3.385Cn1ncc(C(=O)NCc2ccccn2)c1C(=O)Nc3ccn4cc(nc4n3)c5ccccc5
ACDLabs 12.01O=C(NCc1ccccn1)c1cnn(C)c1C(=O)Nc1ccn2cc(nc2n1)c1ccccc1
FormulaC24 H20 N8 O2
Name1-methyl-N~5~-[(4R)-2-phenylimidazo[1,2-a]pyrimidin-7-yl]-N~4~-[(pyridin-2-yl)methyl]-1H-pyrazole-4,5-dicarboxamide
ChEMBL
DrugBank
ZINC
PDB chain5sfj 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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PDB5sfj A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		S677 T688 A689 I692 Y693 M713 E721 V722 G725 Q726 F729
Binding residue
(residue number reindexed from 1)		S219 T230 A231 I234 Y235 M255 E263 V264 G267 Q268 F271
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:5sfj, PDBe:5sfj, PDBj:5sfj
PDBsum5sfj
PubMed36153472
UniProtQ9Y233|PDE10_HUMAN cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (Gene Name=PDE10A)

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