Structure of PDB 6ez6 Chain A Binding Site BS01

Receptor Information
>6ez6 Chain A (length=863) 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
VRGNPNTESAAALVIYLPEVAPHPVYFPALEKILELGRHGERGRITEEEQ
LQLREILERGELYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDV
AQMLYLLCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQY
LLQLVQVLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVA
LRFGLIMEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQT
KEMMHMCMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWI
MYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMT
PYGCLPTGDRTGLIEVVLHSDTIANIQLNKSNMAATAAFNKDALLNWLKS
KNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHID
FGHFLGNRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRR
HGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKF
NEALRESWKTKVN
Ligand information
Ligand IDC5Z
InChIInChI=1S/C26H30N6O4/c1-16(2)32-7-5-31(6-8-32)15-19-13-28-25(36-19)20-9-17(11-23-22(20)14-29-30-23)18-10-21(26(33)35-4)24(34-3)27-12-18/h9-14,16H,5-8,15H2,1-4H3,(H,29,30)
InChIKeyRKURWVGLSOZAMD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)c1cc(cnc1OC)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)OC
FormulaC26 H30 N6 O4
Namemethyl 2-methoxy-5-[4-[5-[(4-propan-2-ylpiperazin-1-yl)methyl]-1,3-oxazol-2-yl]-2~{H}-indazol-6-yl]pyridine-3-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain6ez6 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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PDB6ez6 Selectively Targeting the Kinome-Conserved Lysine of PI3K delta as a General Approach to Covalent Kinase Inhibition.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		S754 W760 I777 K779 D787 I825 V827 M900 D911
Binding residue
(residue number reindexed from 1)		S593 W599 I616 K618 D626 I664 V666 M739 D750
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.40,IC50=39.81nM
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:6ez6, PDBe:6ez6, PDBj:6ez6
PDBsum6ez6
PubMed29232121
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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