6P1D

Crystal structure of EGFR with mutant-selective dihydrodibenzodiazepinone allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Optimization of Dibenzodiazepinones as Allosteric Mutant-Selective EGFR Inhibitors.

De Clercq, D.J.H.Heppner, D.E.To, C.Jang, J.Park, E.Yun, C.H.Mushajiang, M.Shin, B.H.Gero, T.W.Scott, D.A.Janne, P.A.Eck, M.J.Gray, N.S.

(2019) ACS Med Chem Lett 10: 1549-1553

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00381
  • Primary Citation of Related Structures:  
    6P1D, 6P1L, 6P8Q

  • PubMed Abstract: 

    Allosteric kinase inhibitors represent a promising new therapeutic strategy for targeting kinases harboring oncogenic driver mutations in cancers. Here, we report the discovery, optimization, and structural characterization of allosteric mutant-selective EGFR inhibitors comprising a 5,10-dihydro-11 H -dibenzo[ b , e ][1,4]diazepin-11-one scaffold. Our structure-based medicinal chemistry effort yielded an inhibitor ( 3 ) of the EGFR(L858R/T790M) and EGFR(L858R/T790M/C797S) mutants with an IC 50 of ∼10 nM and high selectivity, as assessed by kinome profiling. Further efforts to develop allosteric dibenzodiazepinone inhibitors may serve as the basis for new therapeutic options for targeting drug-resistant EGFR mutations.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptorA [auth D],
B [auth A],
C [auth B],
D [auth C]
327Homo 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
F [auth D],
H [auth A],
J [auth B],
N [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
NQ1 (Subject of Investigation/LOI)
Query on NQ1

Download Ideal Coordinates CCD File 
E [auth D],
K [auth B],
M [auth C]
10-benzyl-8-fluoro-5,10-dihydro-11H-dibenzo[b,e][1,4]diazepin-11-one
C20 H15 F N2 O
NKFCUHMOEKHJLB-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth D],
I [auth A],
L [auth B],
O [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NQ1 BindingDB:  6P1D IC50: min: 39, max: 1.00e+4 (nM) from 9 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.946α = 90
b = 101.812β = 101.04
c = 86.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
DIALSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description