Structure of PDB 5ryd Chain A Binding Site BS01

Receptor Information
>5ryd 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 IDWKV
InChIInChI=1S/C10H12BrNO2/c1-7(13)12-6-8-5-9(11)3-4-10(8)14-2/h3-5H,6H2,1-2H3,(H,12,13)
InChIKeyXPAXEIBSVZPJBZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(Br)cc1CNC(C)=O
OpenEye OEToolkits 2.0.7CC(=O)NCc1cc(ccc1OC)Br
ACDLabs 12.01C(c1c(OC)ccc(c1)Br)NC(=O)C
FormulaC10 H12 Br N O2
NameN-[(5-bromo-2-methoxyphenyl)methyl]acetamide
ChEMBL
DrugBank
ZINCZINC000058217551
PDB chain5ryd 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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PDB5ryd INPP5D PanDDA analysis group deposition
Resolution1.6 Å
Binding residue
(original residue number in PDB)		T478 V479 I504
Binding residue
(residue number reindexed from 1)		T82 V83 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:5ryd, PDBe:5ryd, PDBj:5ryd
PDBsum5ryd
PubMed38309262
UniProtQ92835|SHIP1_HUMAN Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 (Gene Name=INPP5D)

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