Structure of PDB 3x0c Chain B Binding Site BS01

Receptor Information
>3x0c Chain B (length=305) 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
EQFGPGEFDPSVDVYAMKSHESSPKKEVYFMAIADILTPEQYSKRFNEFM
SNILT
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[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)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain3x0c Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3x0c The Lipid Kinase PI5P4K beta Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis
Resolution2.55 Å
Binding residue
(original residue number in PDB)		Y98 S154 A158 H161 R188 Y197
Binding residue
(residue number reindexed from 1)		Y66 S113 A117 H120 R147 Y156
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3x0c, PDBe:3x0c, PDBj:3x0c
PDBsum3x0c
PubMed26774281
UniProtP78356|PI42B_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (Gene Name=PIP4K2B)

[Back to BioLiP]