Structure of PDB 6pys Chain A Binding Site BS01

Receptor Information
>6pys Chain A (length=890) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDL
NSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSDKQKYTL
KINHDCVPEQVIAEAIRKKTRSMYQGKYILKVCGCDEYFLEKYPLSQYKY
IRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRTSTKSLWVINSAL
RIKILCATYVNVNIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWL
NYDIYIPDLPRAARLCLSICSVEEHCPLAWGNINLFDYTDTLVSGKMALN
LWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEE
HANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEIT
EQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIK
PEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQY
LDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRA
CGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDF
MDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLF
QNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDC
VGLIEVVRNSHTIMQIQCKNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAG
YCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHRERVPFVLTQDFL
IVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMP
ELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGW
Ligand information
Ligand IDP5J
InChIInChI=1S/C27H22N6O/c1-17-28-14-20(15-29-17)23-10-11-33-25(31-23)21(16-30-33)19-8-9-24-22(12-19)27(2,26(34)32-24)13-18-6-4-3-5-7-18/h3-12,14-16H,13H2,1-2H3,(H,32,34)/t27-/m0/s1
InChIKeyKQGDDLRQLMABOG-MHZLTWQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(cn1)c2ccn3ncc(c4ccc5NC(=O)[C@@](C)(Cc6ccccc6)c5c4)c3n2
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)c2ccn3c(n2)c(cn3)c4ccc5c(c4)C(C(=O)N5)(C)Cc6ccccc6
CACTVS 3.385Cc1ncc(cn1)c2ccn3ncc(c4ccc5NC(=O)[C](C)(Cc6ccccc6)c5c4)c3n2
ACDLabs 12.01c1(nc2c(cnn2cc1)c3ccc4NC(C(C)(c4c3)Cc5ccccc5)=O)c6cnc(nc6)C
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)c2ccn3c(n2)c(cn3)c4ccc5c(c4)[C@](C(=O)N5)(C)Cc6ccccc6
FormulaC27 H22 N6 O
Name(3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one
ChEMBLCHEMBL4452905
DrugBank
ZINC
PDB chain6pys 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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PDB6pys Design of selective PI3K delta inhibitors using an iterative scaffold-hopping workflow.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		M772 S774 W780 I800 K802 Y836 I848 V851 T856 M922 I932
Binding residue
(residue number reindexed from 1)		M628 S630 W636 I656 K658 Y692 I704 V707 T712 M769 I779
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.15,IC50=70nM
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:6pys, PDBe:6pys, PDBj:6pys
PDBsum6pys
PubMed31416665
UniProtP42336|PK3CA_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (Gene Name=PIK3CA)

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