Structure of PDB 6osp Chain B Binding Site BS01

Receptor Information
>6osp Chain B (length=310) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLYFQSMDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNH
LFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDRF
HTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRL
NVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSAREASDKEKAKELPTLKDN
DFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERA
EQELAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYTVNPEQYSK
RFLDFIGHIL
Ligand information
Ligand IDN51
InChIInChI=1S/C31H29N7O2/c1-38(2)16-6-11-30(39)36-22-14-12-21(13-15-22)31(40)37-24-8-5-7-23(17-24)35-29-18-28(33-20-34-29)26-19-32-27-10-4-3-9-25(26)27/h3-15,17-20,32H,16H2,1-2H3,(H,36,39)(H,37,40)(H,33,34,35)/b11-6+
InChIKeyMJJJRRMQCUUKEO-IZZDOVSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN(C)C/C=C/C(=O)Nc1ccc(cc1)C(=O)Nc2cccc(c2)Nc3cc(ncn3)c4c[nH]c5c4cccc5
ACDLabs 12.01N(C([C@H]=CCN(C)C)=O)c1ccc(cc1)C(=O)Nc5cc(Nc2cc(ncn2)c4cnc3c4cccc3)ccc5
OpenEye OEToolkits 2.0.7CN(C)CC=CC(=O)Nc1ccc(cc1)C(=O)Nc2cccc(c2)Nc3cc(ncn3)c4c[nH]c5c4cccc5
CACTVS 3.385CN(C)C\C=C\C(=O)Nc1ccc(cc1)C(=O)Nc2cccc(Nc3cc(ncn3)c4c[nH]c5ccccc45)c2
CACTVS 3.385CN(C)CC=CC(=O)Nc1ccc(cc1)C(=O)Nc2cccc(Nc3cc(ncn3)c4c[nH]c5ccccc45)c2
FormulaC31 H29 N7 O2
Name4-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}-N-(3-{[6-(1H-indol-3-yl)pyrimidin-4-yl]amino}phenyl)benzamide
ChEMBLCHEMBL4446338
DrugBank
ZINC
PDB chain6osp Chain B Residue 4001 [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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PDB6osp Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		K140 I143 K145 N198 V199 F200 L277
Binding residue
(residue number reindexed from 1)		K106 I109 K111 N164 V165 F166 L241
Annotation score1
Binding affinityMOAD: ic50=190nM
BindingDB: IC50=950nM
Enzymatic activity
Catalytic site (original residue number in PDB) K145 D273
Catalytic site (residue number reindexed from 1) K111 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: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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6osp, PDBe:6osp, PDBj:6osp
PDBsum6osp
PubMed32130941
UniProtP48426|PI42A_HUMAN Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (Gene Name=PIP4K2A)

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