4YKN

Pi3K alpha lipid kinase with Active Site Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Discovery of a Potent Class of PI3K alpha Inhibitors with Unique Binding Mode via Encoded Library Technology (ELT).

Yang, H., Medeiros, P.F., Raha, K., Elkins, P., Lind, K.E., Lehr, R., Adams, N.D., Burgess, J.L., Schmidt, S.J., Knight, S.D., Auger, K.R., Schaber, M.D., Franklin, G.J., Ding, Y., DeLorey, J.L., Centrella, P.A., Mataruse, S., Skinner, S.R., Clark, M.A., Cuozzo, J.W., Evindar, G.

(2015) Acs Med.Chem.Lett. 6: 531-536

  • DOI: 10.1021/acsmedchemlett.5b00025

  • PubMed Abstract: 

    • In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isofor ...

    In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.

    Related Citations: 
    • Baculovirus production of fully-active phosphoinositide 3-kinase alpha as a p85a-p110a fusion for X-ray crystallographic analysis with ATP competitive enzyme inhibitors
      Sinnamon, R.H.,McDevitt, P.,Pietrak, B.L.,Leydon, V.R.,Xue, Y.,Lehr, R.,Qi, H.,Burns, M.,Elkins, P.,Ward, P.,Vincentini, G.,Fisher, D.,Grimes, M.,Brandt, M.,Auger, K.R.,Ho, T.,Johanson, K.,Jones, C.S.,Schwartz, B.,Sweitzer, T.D.,Kirkpatrick, R.B.
      (2010) PROTEIN EXPR.PURIF. 73: 167

    Organizational Affiliation: 

    Computational and Structural Chemistry, Platform Technology and Science, Biological Reagents and Assay Development, Platform Technology and Science, Oncology Research, and Screening and Compound Profiling, Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.,MDR (Molecular Discovery Research) Boston, Platform Technology and Science, GlaxoSmithKline , 830 Winter Street, Waltham, Massachusetts 02451, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha,Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform fusion protein
A
1383Homo sapiensMutation(s): 0 
Gene Names: PIK3CA, PIK3R1 (GRB1)
EC: 2.7.1.153
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4EL
Query on 4EL
Download SDF File 
Download CCD File 
A
3-(6-methoxypyridin-3-yl)-5-[({4-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl}amino)methyl]benzoic acid
C23 H21 N5 O5 S2
CBZPCOUPBNLTKW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4ELIC50: 8.5 - 10 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.667α = 90.00
b = 118.191β = 90.00
c = 190.281γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-03-04 
  • Released Date: 2015-06-17 
  • Deposition Author(s): Elkins, P.A.

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy