Structure of PDB 3x05 Chain A Binding Site BS01

Receptor Information
>3x05 Chain A (length=320) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNH
LFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINTRFL
TTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLT
VDGVETYMVVMRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKD
NDFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDR
AEQEEMEVEERAEDGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTP
TVNPEQYSKRFNEFMSNILT
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain3x05 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3x05 The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F139 K150 N203 V204 K214 L282 I368 D369
Binding residue
(residue number reindexed from 1)		F99 K110 N163 V164 K174 L242 I295 D296
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K150 D278
Catalytic site (residue number reindexed from 1) K110 D238
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:3x05, PDBe:3x05, PDBj:3x05
PDBsum3x05
PubMed26774281
UniProtP78356|PI42B_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (Gene Name=PIP4K2B)

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