4RJ3

CDK2 with EGFR inhibitor compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/jm501578n
  • Primary Citation of Related Structures:  

  • 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 inhibitor ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
3QS
Query on 3QS

Download SDF File 
Download CCD File 
A
1-cyclopentyl-N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-1H-pyrrolo[3,2-c]pyridin-6-amine
C22 H28 N6 O
BYMFSZLMPVZBJV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3QSIC50: 93 nM (100) BINDINGDB
3QSIC50: 93 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.102α = 90.00
b = 70.923β = 90.00
c = 72.586γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
B3data collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-08 
  • Released Date: 2014-11-26 
  • Deposition Author(s): Eigenbrot, C., Yin, J.

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references