Structure of PDB 7n7n Chain A Binding Site BS01

Receptor Information
>7n7n Chain A (length=303) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKEN
MPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDARFHTSYD
KRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGV
EIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFI
NEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAGEF
DPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKVNPEQYSKRFLDFIG
HIL
Ligand information
Ligand IDIBI
InChIInChI=1S/C34H50N8O3/c1-6-28-33(44)39(4)29-20-35-34(38-31(29)42(28)22(2)3)37-27-14-9-24(19-30(27)45-5)32(43)36-25-10-12-26(13-11-25)41-17-15-40(16-18-41)21-23-7-8-23/h9,14,19-20,22-23,25-26,28H,6-8,10-13,15-18,21H2,1-5H3,(H,36,43)(H,35,37,38)/t25-,26-,28-/m1/s1
InChIKeySXNJFOWDRLKDSF-STROYTFGSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC[CH]1N(C(C)C)c2nc(Nc3ccc(cc3OC)C(=O)N[CH]4CC[CH](CC4)N5CCN(CC5)CC6CC6)ncc2N(C)C1=O
OpenEye OEToolkits 1.5.0CCC1C(=O)N(c2cnc(nc2N1C(C)C)Nc3ccc(cc3OC)C(=O)NC4CCC(CC4)N5CCN(CC5)CC6CC6)C
OpenEye OEToolkits 1.5.0CC[C@@H]1C(=O)N(c2cnc(nc2N1C(C)C)Nc3ccc(cc3OC)C(=O)NC4CCC(CC4)N5CCN(CC5)CC6CC6)C
CACTVS 3.341CC[C@H]1N(C(C)C)c2nc(Nc3ccc(cc3OC)C(=O)N[C@H]4CC[C@@H](CC4)N5CCN(CC5)CC6CC6)ncc2N(C)C1=O
ACDLabs 10.04O=C6N(c1c(nc(nc1)Nc2ccc(cc2OC)C(=O)NC5CCC(N3CCN(CC3)CC4CC4)CC5)N(C(C)C)C6CC)C
FormulaC34 H50 N8 O3
NameN-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide;
Volasertib
ChEMBLCHEMBL1233528
DrugBankDB12062
ZINC
PDB chain7n7n Chain A Residue 501 [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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PDB7n7n Pharmacological inhibition of PI5P4K alpha / beta disrupts cell energy metabolism and selectively kills p53-null tumor cells.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F134 I143 K145 N198 V199 F200 L230 I358 D359
Binding residue
(residue number reindexed from 1)		F95 I104 K106 N159 V160 F161 L191 I276 D277
Annotation score1
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: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:0010506 regulation of autophagy
GO:0016310 phosphorylation
GO:0035855 megakaryocyte development
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:0090119 vesicle-mediated cholesterol transport
GO:1902635 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
GO:2000786 positive regulation of autophagosome assembly
Cellular Component
GO:0001750 photoreceptor outer segment
GO:0001917 photoreceptor inner segment
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0042995 cell projection

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7n7n, PDBe:7n7n, PDBj:7n7n
PDBsum7n7n
PubMed34001596
UniProtP48426|PI42A_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (Gene Name=PIP4K2A)

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