5EM8

EGFR kinase domain with pyridone compound 13: 4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyridones as Highly Selective, Noncovalent Inhibitors of T790M Double Mutants of EGFR.

Bryan, M.C.Burdick, D.J.Chan, B.K.Chen, Y.Clausen, S.Dotson, J.Eigenbrot, C.Elliott, R.Hanan, E.J.Heald, R.Jackson, P.La, H.Lainchbury, M.Malek, S.Mann, S.E.Purkey, H.E.Schaefer, G.Schmidt, S.Seward, E.Sideris, S.Wang, S.Yen, I.Yu, C.Heffron, T.P.

(2016) ACS Med Chem Lett 7: 100-104

  • DOI: 10.1021/acsmedchemlett.5b00428
  • Primary Citation of Related Structures:  
    5EM6, 5EM5, 5EM8, 5EM7

  • PubMed Abstract: 
  • The rapid advancement of a series of noncovalent inhibitors of T790M mutants of EGFR is discussed. The optimization of pyridone 1, a nonselective high-throughput screening hit, to potent molecules with high levels of selectivity over wtEGFR and the broad ...

    The rapid advancement of a series of noncovalent inhibitors of T790M mutants of EGFR is discussed. The optimization of pyridone 1, a nonselective high-throughput screening hit, to potent molecules with high levels of selectivity over wtEGFR and the broader kinome is described herein.


    Organizational Affiliation

    Genentech , South San Francisco, California 94080, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptor A331Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS:  P00533
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5Q4
Query on 5Q4

Download Ideal Coordinates CCD File 
A
4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide
C24 H27 N5 O3
DWKPGVACBGLMCU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Q4Ki:  1090   nM  BindingDB
5Q4EC50:  1090   nM  BindingDB
5Q4Ki:  19   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.661α = 90
b = 147.661β = 90
c = 147.661γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-11-05 
  • Released Date: 2015-12-30 
  • Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Data collection, Derived calculations