5CAP

EGFR kinase domain mutant "TMLR" with compound 30

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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This is version 1.2 of the entry. See complete history. 


Literature

Noncovalent Mutant Selective Epidermal Growth Factor Receptor Inhibitors: A Lead Optimization Case Study.

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

(2015) J Med Chem 58: 8877-8895

  • DOI: 10.1021/acs.jmedchem.5b01412
  • Primary Citation of Related Structures:  
    5C8K, 5C8M, 5C8N, 5CAL, 5CAN, 5CAO, 5CAP, 5CAQ, 5CAS, 5CAU, 5CAV

  • PubMed Abstract: 

    • Because of their increased activity against activating mutants, first-generation epidermal growth factor receptor (EGFR) kinase inhibitors have had remarkable success in treating non-small-cell lung cancer (NSCLC) patients, but acquired resistance, through a secondary mutation of the gatekeeper residue, means that clinical responses only last for 8-14 months ...

    Because of their increased activity against activating mutants, first-generation epidermal growth factor receptor (EGFR) kinase inhibitors have had remarkable success in treating non-small-cell lung cancer (NSCLC) patients, but acquired resistance, through a secondary mutation of the gatekeeper residue, means that clinical responses only last for 8-14 months. Addressing this unmet medical need requires agents that can target both of the most common double mutants: T790M/L858R (TMLR) and T790M/del(746-750) (TMdel). Herein we describe how a noncovalent double mutant selective lead compound was optimized using a strategy focused on the structure-guided increase in potency without added lipophilicity or reduction of three-dimensional character. Following successive rounds of design and synthesis it was discovered that cis-fluoro substitution on 4-hydroxy- and 4-methoxypiperidinyl groups provided synergistic, substantial, and specific potency gain through direct interaction with the enzyme and/or effects on the proximal ligand oxygen atom. Further development of the fluorohydroxypiperidine series resulted in the identification of a pair of diastereomers that showed 50-fold enzyme and cell based selectivity for T790M mutants over wild-type EGFR (wtEGFR) in vitro and pathway knock-down in an in vivo xenograft model.

    Organizational Affiliation: 

    Argenta, Early Discovery Charles River , 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4ZH
Query on 4ZH
Download Ideal Coordinates CCD File 
D [auth A]2-methyl-N-[2-(2-methyl-2-methylsulfonyl-propoxy)pyrimidin-4-yl]-1-propan-2-yl-imidazo[4,5-c]pyridin-6-amine
C19 H26 N6 O3 S
SHYWETJFHVMCJS-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4ZH Binding MOAD:  5CAP Ki: 52 (nM) from 1 assay(s)
BindingDB:  5CAP Ki: min: 52, max: 2100 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.007α = 90
b = 149.007β = 90
c = 149.007γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2015-06-29 
  • Released Date: 2015-10-28 
    • Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references