Structure of PDB 6dgt Chain A Binding Site BS01

Receptor Information
>6dgt Chain A (length=777) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLINSQISLLIGKGLDSLRDPEVNDFRTKMRQFCEEAAAHRQQLGWVEWL
QYSFPLQLEPALLVNVKFEEESFTFQVSTKDMPLALMACALRQPEEYALQ
VNGRHEYLYPLCHFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNSLEQ
PFSIELIEGRKVMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLE
FDISVCDLPRMARLCFALYAVVCPIAWANLMLFDYKDQLKTGERCLYMWP
SVLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALEKILELYEHEKDL
VWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSAL
ELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELT
KFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMK
VLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSH
LQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKN
GDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLH
SDTIANIQLNAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATY
VLGIGDRHSDNIMIRESGQLFHIDFGHFLGNVPFILTYDFVHVIQQGKTN
NSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYL
KDSLALGKTEEEALKHFRVKFNEALRE
Ligand information
Ligand IDGFJ
InChIInChI=1S/C24H15F3N8/c1-11-33-21-14(24-31-10-32-34-24)8-12(13-4-6-30-23(28)20(13)27)9-18(21)35(11)17-5-7-29-22-16(26)3-2-15(25)19(17)22/h2-10H,1H3,(H2,28,30)(H,31,32,34)
InChIKeySBVBUGSOYHJGGD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nc2c(cc(cc2c3[nH]cnn3)c4ccnc(N)c4F)n1c5ccnc6c(F)ccc(F)c56
OpenEye OEToolkits 2.0.6Cc1nc2c(cc(cc2n1c3ccnc4c3c(ccc4F)F)c5ccnc(c5F)N)c6[nH]cnn6
ACDLabs 12.01n3c5c(n(c1c2c(ncc1)c(ccc2F)F)c3C)cc(c4c(c(N)ncc4)F)cc5c6nncn6
FormulaC24 H15 F3 N8
Name4-[1-(5,8-difluoroquinolin-4-yl)-2-methyl-4-(4H-1,2,4-triazol-3-yl)-1H-benzimidazol-6-yl]-3-fluoropyridin-2-amine
ChEMBLCHEMBL4470860
DrugBank
ZINC
PDB chain6dgt Chain A Residue 1101 [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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PDB6dgt Atropisomerism by Design: Discovery of a Selective and Stable Phosphoinositide 3-Kinase (PI3K) beta Inhibitor.
Resolution2.601 Å
Binding residue
(original residue number in PDB)		M752 P758 I777 K779 D787 I825 V827 V828 M900 D911
Binding residue
(residue number reindexed from 1)		M522 P528 I547 K549 D557 I595 V597 V598 M663 D674
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.38,IC50=42nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6dgt, PDBe:6dgt, PDBj:6dgt
PDBsum6dgt
PubMed30015489
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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