Structure of PDB 4ajw Chain B Binding Site BS01

Receptor Information
>4ajw Chain B (length=792) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWV
EWLQYSFPLQLEPSAVSNRALLVNVKFEGSEESFTFQVSTKDMPLALMAC
ALRKKATVQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLTM
VHSSSILAMRDEQSNEQPFSIELIEGRKVNAMKLVVQAGLFHGNEMLCKT
VSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYADCPIAWANLML
FDYKDQLKTGERCLYMWPSLLNPAGTVRGNPNTESAAALVIYLPEVAPVY
FPALEKILELEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQM
LYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQ
LVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRF
GLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEM
MHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYS
SEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYG
CLPTGDRTGLIEVVLHSDTIANIQLTAAFNKDALLNWLKSKNPGEALDRA
IEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGPFIL
TYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAA
GLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES
Ligand information
Ligand IDVWN
InChIInChI=1S/C17H19N5O2/c1-21-13-5-3-2-4-12(13)18-15(21)10-14-19-16(11-17(23)20-14)22-6-8-24-9-7-22/h2-5,11H,6-10H2,1H3,(H,19,20,23)
InChIKeyXLESLWHDVUIEMT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cn1c2ccccc2nc1CC3=NC(=CC(=O)N3)N4CCOCC4
CACTVS 3.385Cn1c(CC2=NC(=CC(=O)N2)N3CCOCC3)nc4ccccc14
ACDLabs 12.01O=C1C=C(N=C(N1)Cc3nc2ccccc2n3C)N4CCOCC4
FormulaC17 H19 N5 O2
Name2-[(1-methyl-1H-benzimidazol-2-yl)methyl]-6-morpholin-4-ylpyrimidin-4(3H)-one
ChEMBLCHEMBL2064330
DrugBank
ZINCZINC000084727627
PDB chain4ajw Chain B Residue 2027 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ajw Discovery and Optimization of New Benzimidazole- and Benzoxazole-Pyrimidone Selective Pi3Kbeta Inhibitors for the Treatment of Phosphatase and Tensin Homologue (Pten)-Deficient Cancers.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		M752 P758 W760 I777 Y813 V828
Binding residue
(residue number reindexed from 1)		M538 P544 W546 I563 Y599 V614
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.1.137: phosphatidylinositol 3-kinase.
2.7.1.153: phosphatidylinositol-4,5-bisphosphate 3-kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity
Biological Process
GO:0001782 B cell homeostasis
GO:0002250 adaptive immune response
GO:0006629 lipid metabolic process
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0007166 cell surface receptor signaling pathway
GO:0010628 positive regulation of gene expression
GO:0016310 phosphorylation
GO:0030154 cell differentiation
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0042113 B cell activation
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0045087 innate immune response
GO:0045766 positive regulation of angiogenesis
GO:0046854 phosphatidylinositol phosphate biosynthetic process
GO:0048872 homeostasis of number of cells
GO:0050832 defense response to fungus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ajw, PDBe:4ajw, PDBj:4ajw
PDBsum4ajw
PubMed22524426
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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