Structure of PDB 5ry9 Chain A Binding Site BS02

Receptor Information
>5ry9 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 IDWKS
InChIInChI=1S/C10H16N4/c1-8-7-10(13-9(2)12-8)14-5-3-11-4-6-14/h7,11H,3-6H2,1-2H3
InChIKeyNARMKNJWXHFJFF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc(nc(n1)C)N2CCNCC2
ACDLabs 12.01C1CNCCN1c2cc(C)nc(n2)C
CACTVS 3.385Cc1cc(nc(C)n1)N2CCNCC2
FormulaC10 H16 N4
Name2,4-dimethyl-6-(piperazin-1-yl)pyrimidine
ChEMBL
DrugBank
ZINCZINC000004945061
PDB chain5ry9 Chain A Residue 902 [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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PDB5ry9 INPP5D PanDDA analysis group deposition
Resolution1.52 Å
Binding residue
(original residue number in PDB)
H503 M528 G565 D566
Binding residue
(residue number reindexed from 1)
H107 M132 G169 D170
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

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Molecular Function

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Biological Process
External links
PDB RCSB:5ry9, PDBe:5ry9, PDBj:5ry9
PDBsum5ry9
PubMed38309262
UniProtQ92835|SHIP1_HUMAN Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 (Gene Name=INPP5D)

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