7B85

Crystal Structure of EGFR-WT in Complex with TAK-788


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Insight into Targeting Exon20 Insertion Mutations of the Epidermal Growth Factor Receptor with Wild Type-Sparing Inhibitors.

Lategahn, J.Tumbrink, H.L.Schultz-Fademrecht, C.Heimsoeth, A.Werr, L.Niggenaber, J.Keul, M.Parmaksiz, F.Baumann, M.Menninger, S.Zent, E.Landel, I.Weisner, J.Jeyakumar, K.Heyden, L.Russ, N.Muller, F.Lorenz, C.Bragelmann, J.Spille, I.Grabe, T.Muller, M.P.Heuckmann, J.M.Klebl, B.M.Nussbaumer, P.Sos, M.L.Rauh, D.

(2022) J Med Chem 65: 6643-6655

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02080
  • Primary Citation of Related Structures:  
    7A6I, 7A6J, 7A6K, 7B85

  • PubMed Abstract: 

    Despite the clinical efficacy of epidermal growth factor receptor (EGFR) inhibitors, a subset of patients with non-small cell lung cancer displays insertion mutations in exon20 in EGFR and Her2 with limited treatment options. Here, we present the development and characterization of the novel covalent inhibitors LDC8201 and LDC0496 based on a 1 H -pyrrolo[2,3- b ]pyridine scaffold. They exhibited intense inhibitory potency toward EGFR and Her2 exon20 insertion mutations as well as selectivity over wild type EGFR and within the kinome. Complex crystal structures with the inhibitors and biochemical and cellular on-target activity document their favorable binding characteristics. Ultimately, we observed tumor shrinkage in mice engrafted with patient-derived EGFR-H773_V774insNPH mutant cells during treatment with LDC8201. Together, these results highlight the potential of covalent pyrrolopyridines as inhibitors to target exon20 insertion mutations.


  • Organizational Affiliation

    PearlRiver Bio GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor333Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R28 (Subject of Investigation/LOI)
Query on R28

Download Ideal Coordinates CCD File 
B [auth A]propan-2-yl 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]-2-methoxy-5-(propanoylamino)phenyl]amino]-4-(1-methylindol-3-yl)pyrimidine-5-carboxylate
C32 H41 N7 O4
CINKQTDSFCVDKO-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.28α = 90
b = 144.28β = 90
c = 144.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyBMBF 01GS08104
German Federal Ministry for Education and ResearchGermanyBMBF 01ZX1303C
European Regional Development FundGermanyEFRE-800400

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2022-10-05
    Changes: Structure summary
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description