Structure of PDB 5ryl Chain A Binding Site BS01

Receptor Information
>5ryl Chain A (length=460) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIY
VIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPE
HENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSE
KKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTW
EAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFE
RLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIM
TSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTK
FYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYL
LDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHF
QGEIKLQTSQ
Ligand information
Ligand IDS7J
InChIInChI=1S/C6H4F3N3O/c7-6(8,9)5-11-1-3(2-12-5)4(10)13/h1-2H,(H2,10,13)
InChIKeyOKRNBFHZDGTDRX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c(cnc(n1)C(F)(F)F)C(=O)N
CACTVS 3.385NC(=O)c1cnc(nc1)C(F)(F)F
FormulaC6 H4 F3 N3 O
Name2-(trifluoromethyl)pyrimidine-5-carboxamide
ChEMBL
DrugBank
ZINCZINC000075847370
PDB chain5ryl Chain A Residue 901 [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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PDB5ryl INPP5D PanDDA analysis group deposition
Resolution1.55 Å
Binding residue
(original residue number in PDB)		K477 T478 V479 E498 I501 I504
Binding residue
(residue number reindexed from 1)		K81 T82 V83 E102 I105 I108
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.3.36: phosphoinositide 5-phosphatase.
3.1.3.56: inositol-polyphosphate 5-phosphatase.
3.1.3.86: phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase.
Gene Ontology
Molecular Function
GO:0016791 phosphatase activity
Biological Process
GO:0046856 phosphatidylinositol dephosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ryl, PDBe:5ryl, PDBj:5ryl
PDBsum5ryl
PubMed38309262
UniProtQ92835|SHIP1_HUMAN Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 (Gene Name=INPP5D)

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