EGFR kinase (T790M/L858R) with inhibitor compound 1

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of Selective and Noncovalent Diaminopyrimidine-Based Inhibitors of Epidermal Growth Factor Receptor Containing the T790M Resistance Mutation.

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

(2014) J Med Chem 57: 10176-10191

  • DOI: https://doi.org/10.1021/jm501578n
  • Primary Citation of Related Structures:  
    4RJ3, 4RJ4, 4RJ5, 4RJ6, 4RJ7, 4RJ8

  • PubMed Abstract: 

    Activating mutations within the epidermal growth factor receptor (EGFR) kinase domain, commonly L858R or deletions within exon 19, increase EGFR-driven cell proliferation and survival and are correlated with impressive responses to the EGFR inhibitors erlotinib and gefitinib in nonsmall cell lung cancer patients. Approximately 60% of acquired resistance to these agents is driven by a single secondary mutation within the EGFR kinase domain, specifically substitution of the gatekeeper residue threonine-790 with methionine (T790M). Due to dose-limiting toxicities associated with inhibition of wild-type EGFR (wtEGFR), we sought inhibitors of T790M-containing EGFR mutants with selectivity over wtEGFR. We describe the evolution of HTS hits derived from Jak2/Tyk2 inhibitors into selective EGFR inhibitors. X-ray crystal structures revealed two distinct binding modes and enabled the design of a selective series of novel diaminopyrimidine-based inhibitors with good potency against T790M-containing mutants of EGFR, high selectivity over wtEGFR, broad kinase selectivity, and desirable physicochemical properties.

  • Organizational Affiliation

    Departments of †Discovery Chemistry, ‡Structural Biology, §Drug Metabolism and Pharmacokinetics, ∥Biochemical and Cellular Pharmacology, ⊥Molecular Oncology, and #Protein Expression, Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3R1

Download Ideal Coordinates CCD File 
C [auth A]2,6-dichloro-N-{2-[(2-{[(2S)-1-hydroxypropan-2-yl]amino}-6-methylpyrimidin-4-yl)amino]pyridin-4-yl}benzamide
C20 H20 Cl2 N6 O2
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
3R1 BindingDB:  4RJ7 Ki: min: 9, max: 101 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.605α = 90
b = 146.605β = 90
c = 146.605γ = 90
Software Package:
Software NamePurpose
B3data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description