Structure of PDB 3zim Chain A Binding Site BS01

Receptor Information
>3zim Chain A (length=886) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDL
NSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQK
YTLKINHDCVPEQVIAEAIRKKTRSMLEYQGKYILKVCGCDEYFLEKYPL
SQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRKSLWVINS
ALRIKILCATYVNVNDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEW
LNYDIYIPDLPRAARLCLSICSHCPLAWGNINLFDYTDTLVSGKMALNLW
PVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHA
NWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQ
EKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPE
QAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLD
NLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACG
MYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMD
ALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQN
NEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVG
LIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDL
FTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDRERVPFV
LTQDFLIVISCTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGM
PELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDA
Ligand information
Ligand IDKKR
InChIInChI=1S/C30H35N7O3S/c1-20(2)16-21(38)6-7-27(39)36-10-8-35(9-11-36)19-22-17-26-28(41-22)30(37-12-14-40-15-13-37)33-29(32-26)23-4-3-5-25-24(23)18-31-34-25/h3-5,16-18H,6-15,19H2,1-2H3,(H,31,34)
InChIKeyDLNUPKDFXMWRFP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(=CC(=O)CCC(=O)N1CCN(CC1)Cc2cc3c(s2)c(nc(n3)c4cccc5c4cn[nH]5)N6CCOCC6)C
CACTVS 3.385CC(C)=CC(=O)CCC(=O)N1CCN(CC1)Cc2sc3c(c2)nc(nc3N4CCOCC4)c5cccc6[nH]ncc56
ACDLabs 12.01O=C(\C=C(/C)C)CCC(=O)N1CCN(CC1)Cc3sc2c(nc(nc2c3)c5cccc4nncc45)N6CCOCC6
FormulaC30 H35 N7 O3 S
Name1-[4-[[2-(1H-indazol-4-yl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidin-6-yl]methyl]piperazin-1-yl]-6-methyl-hept-5-ene-1,4- dione;
1-[4-[[2-(1H-indazol-4-yl)-4-morpholinthieno[3,2-d]pyrimidin-6-yl]methyl]piperazin-1-yl]-6-methyl-hept-5-ene-1,4-dione
ChEMBLCHEMBL2316958
DrugBank
ZINCZINC000095593683
PDB chain3zim Chain A Residue 2047 [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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PDB3zim Discovery of a Potent and Isoform-Selective Targeted Covalent Inhibitor of the Lipid Kinase Pi3Kalpha
Resolution2.85 Å
Binding residue
(original residue number in PDB)		M772 I800 D810 Y836 I848 E849 V850 V851 Q859 C862 M922 I932 D933
Binding residue
(residue number reindexed from 1)		M626 I654 D664 Y690 I702 E703 V704 V705 Q713 C716 M776 I786 D787
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.17,IC50=6.8nM
BindingDB: IC50=6.8nM,EC50=10nM
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
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
Biological Process
GO:0046854 phosphatidylinositol phosphate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3zim, PDBe:3zim, PDBj:3zim
PDBsum3zim
PubMed23360348
UniProtP42336|PK3CA_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (Gene Name=PIK3CA)

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