Structure of PDB 3x04 Chain A Binding Site BS01

Receptor Information
>3x04 Chain A (length=314) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNH
LFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINRFLT
TYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTV
DGVETYMVVTRNVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDN
DFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRA
EQEEMEVEERAGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILVNPEQ
YSKRFNEFMSNILT
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain3x04 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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PDB3x04 The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Resolution2.6 Å
Binding residue
(original residue number in PDB)		F139 V148 N203 V204 F205 K214 D369
Binding residue
(residue number reindexed from 1)		F98 V107 N162 V163 F164 K173 D293
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K150 D278
Catalytic site (residue number reindexed from 1) K109 D237
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3x04, PDBe:3x04, PDBj:3x04
PDBsum3x04
PubMed26774281
UniProtP78356|PI42B_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (Gene Name=PIP4K2B)

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