5HCY

EGFR kinase domain mutant "TMLR" with 3-carboxamide azaindole compound 13

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


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


Literature

Discovery of a Noncovalent, Mutant-Selective Epidermal Growth Factor Receptor Inhibitor.

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

(2016) J Med Chem 59: 9080-9093

  • DOI: 10.1021/acs.jmedchem.6b00995
  • Primary Citation of Related Structures:  
    5HCX, 5HCY, 5HCZ

  • PubMed Abstract: 

    • Inhibitors targeting the activating mutants of the epidermal growth factor receptor (EGFR) have found success in the treatment of EGFR mutant positive non-small-cell lung cancer. A secondary point mutation (T790M) in the inhibitor binding site has been linked to the acquired resistance against those first generation therapeutics ...

    Inhibitors targeting the activating mutants of the epidermal growth factor receptor (EGFR) have found success in the treatment of EGFR mutant positive non-small-cell lung cancer. A secondary point mutation (T790M) in the inhibitor binding site has been linked to the acquired resistance against those first generation therapeutics. Herein, we describe the lead optimization of a series of reversible, pan-mutant (L858R, del 746-750, T790M/L858R, and T790M/del 746-750 ) EGFR inhibitors. By use of a noncovalent double mutant (T790M/L858R and T790M/del 746-750 ) selective EGFR inhibitor (2) as a starting point, activities against the single mutants (L858R and del 746-750 ) were introduced through a series of structure-guided modifications. The in vitro ADME-PK properties of the lead molecules were further optimized through a number of rational structural changes. The resulting inhibitor (21) exhibited excellent cellular activity against both the single and double mutants of EGFR, demonstrating target engagement in vivo and ADME-PK properties that are suitable for further evaluation. The reversible, noncovalent inhibitors described complement the covalent pan-mutant EGFR inhibitors that have shown encouraging results in recent clinical trials.

    Organizational Affiliation: 

    Charles River Laboratories, 7/9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA331Homo sapiensMutation(s): 5 
Gene Names: EGFR, ERBB, ERBB1, HER1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
60D
Query on 60D
Download Ideal Coordinates CCD File 
C [auth A]6-[[2-(1-cyclopropylsulfonylpyrazol-4-yl)pyrimidin-4-yl]amino]-~{N}-(oxan-4-yl)-1-propan-2-yl-pyrrolo[3,2-c]pyridine-3-carboxamide
C26 H30 N8 O4 S
DJHWPKSBDIEQGY-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
60D Binding MOAD:  5HCY Ki: 1.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.6α = 90
b = 146.6β = 90
c = 146.6γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2016-01-04 
  • Released Date: 2016-09-07 
    • Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references