VOOZH about

URL: https://www.rcsb.org/structure/3ZIM

⇱ RCSB PDB - 3ZIM: Discovery of a potent and isoform-selective targeted covalent inhibitor of the lipid kinase PI3Kalpha

👁 RCSB PDB
251,806
Structures from the PDB archive		1,068,577
Computed Structure Models (CSM)

 3ZIM | pdb_00003zim

Discovery of a potent and isoform-selective targeted covalent inhibitor of the lipid kinase PI3Kalpha

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Discovery of a Potent and Isoform-Selective Targeted Covalent Inhibitor of the Lipid Kinase Pi3Kalpha

Nacht, M., Qiao, L., Sheets, M.P., Martin, T.S., Labenski, M., Mazdiyasni, H., Karp, R., Zhu, Z., Chaturvedi, P., Bhavsar, D., Niu, D., Westlin, W., Petter, R.C., Medikonda, A.P., Singh, J.

(2013) J Med Chem 56: 712

  • PubMed: 23360348 Search on PubMed
  • DOI: https://doi.org/10.1021/jm3008745
  • Primary Citation Related Structures: 
    3ZIM

  • PubMed Abstract: 

    PI3Kα has been identified as an oncogene in human tumors. By use of rational drug design, a targeted covalent inhibitor 3 (CNX-1351) was created that potently and specifically inhibits PI3Kα. We demonstrate, using mass spectrometry and X-ray crystallography, that the selective inhibitor covalently modifies PI3Kα on cysteine 862 (C862), an amino acid unique to the α isoform, and that PI3Kβ, -γ, and -δ are not covalently modified. 3 is able to potently (EC(50) < 100 nM) and specifically inhibit signaling in PI3Kα-dependent cancer cell lines, and this leads to a potent antiproliferative effect (GI(50) < 100 nM). A covalent probe, 8 (CNX-1220), which selectively bonds to PI3Kα, was used to investigate the duration of occupancy of 3 with PI3Kα in vivo. This is the first report of a PI3Kα-selective inhibitor, and these data demonstrate the biological impact of selectively targeting PI3Kα.

    • Organizational Affiliation: 
    • Celgene Avilomics Research, 45 Wiggins Avenue, Bedford, Massachusetts 01730, USA. mnacht@celgene.com

Macromolecule Content 

  • Total Structure Weight: 109.98 kDa 
  • Atom Count: 7,286 
  • Modeled Residue Count: 886 
  • Deposited Residue Count: 940 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT ALPHA ISOFORM940Homo sapiensMutation(s): 0 
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
PHAROS:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KKR
Query on KKR
Download Ideal Coordinates CCD File 
B [auth A]1-[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
C30 H35 N7 O3 S
DLNUPKDFXMWRFP-UHFFFAOYSA-N		👁 Image
Binding Affinity Annotations 
IDSourceBinding Affinity
KKR BindingDB:  3ZIM IC50: 6.8 (nM) from 1 assay(s)
EC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.34α = 90
b = 135.027β = 90
c = 142.921γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report

👁 Image


Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.