Structure of PDB 7em4 Chain B Binding Site BS01

Receptor Information
>7em4 Chain B (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNH
LFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLT
TYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTV
DGVETYMVVTRNVLSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDN
DFLNEGQKLHVKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAFFGP
GEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTPEQYSKRFNEFMSNILT
Ligand information
Ligand IDIDP
InChIInChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyJPXZQMKKFWMMGK-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC=Nc23
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC=Nc23
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=CNC1=O)C(O)C3O
FormulaC10 H14 N4 O11 P2
NameINOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL1233551
DrugBank
ZINCZINC000004261903
PDB chain7em4 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7em4 The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		K150 N203 V204 D216 D369
Binding residue
(residue number reindexed from 1)		K109 N162 V163 D175 D280
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.149: 1-phosphatidylinositol-5-phosphate 4-kinase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016301 kinase activity
GO:0016308 1-phosphatidylinositol-4-phosphate 5-kinase activity
GO:0016309 1-phosphatidylinositol-5-phosphate 4-kinase activity
GO:0042803 protein homodimerization activity
GO:0052742 phosphatidylinositol kinase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0007166 cell surface receptor signaling pathway
GO:0010506 regulation of autophagy
GO:0016310 phosphorylation
GO:0046488 phosphatidylinositol metabolic process
GO:0046627 negative regulation of insulin receptor signaling pathway
GO:0046854 phosphatidylinositol phosphate biosynthetic process
GO:0061909 autophagosome-lysosome fusion
GO:1902635 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
GO:2000786 positive regulation of autophagosome assembly
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005776 autophagosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7em4, PDBe:7em4, PDBj:7em4
PDBsum7em4
PubMed35504278
UniProtP78356|PI42B_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (Gene Name=PIP4K2B)

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