Structure of PDB 6eyz Chain A Binding Site BS01

Receptor Information
>6eyz Chain A (length=862) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRVKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQ
LGWVEWLQYSFPLQLEPSARGNRALLVNVKFEGSEESFTFQVSTKDMPLA
LMACALRKKATVFRQPLVEQPEEYALQVNGRHEYLYGNYPLCHFQYICSC
LHSGLTPHLTMVHSSSILAMRDEQSNPASLWSLEQPFSIELIEGRKVNAD
ERMKLVVQAGLFHGNEMLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPR
MARLCFALYAVVDCPIAWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGT
VRGNPNTESAAALVIYLPEVAPHPVYFPALEKILELGRHGERRITEEEQL
QLREILERGELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVA
QMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYL
LQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVAL
RFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTK
EMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIM
YSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTP
YGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKSK
NPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDF
GHFLGNRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRH
GLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFN
EALRESWKTKVN
Ligand information
Ligand IDC5W
InChIInChI=1S/C25H28N6O4/c1-15(2)31-6-4-30(5-7-31)14-18-12-27-24(35-18)19-8-16(10-22-21(19)13-28-29-22)17-9-20(25(32)33)23(34-3)26-11-17/h8-13,15H,4-7,14H2,1-3H3,(H,28,29)(H,32,33)
InChIKeyCPVGTJFGSVAPTE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ncc(cc1C(O)=O)c2cc3n[nH]cc3c(c2)c4oc(CN5CCN(CC5)C(C)C)cn4
OpenEye OEToolkits 2.0.6CC(C)N1CCN(CC1)Cc2cnc(o2)c3cc(cc4c3c[nH]n4)c5cc(c(nc5)OC)C(=O)O
FormulaC25 H28 N6 O4
Name2-methoxy-5-[4-[5-[(4-propan-2-ylpiperazin-1-yl)methyl]-1,3-oxazol-2-yl]-2~{H}-indazol-6-yl]pyridine-3-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6eyz 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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PDB6eyz Selectively Targeting the Kinome-Conserved Lysine of PI3K delta as a General Approach to Covalent Kinase Inhibition.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		M752 W760 I777 K779 D787 I825 V827 V828 M900 D911
Binding residue
(residue number reindexed from 1)		M590 W598 I615 K617 D625 I663 V665 V666 M738 D749
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,IC50=7.94nM
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:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
Biological Process
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0046854 phosphatidylinositol phosphate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6eyz, PDBe:6eyz, PDBj:6eyz
PDBsum6eyz
PubMed29232121
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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