6P1D | pdb_00006p1d

Crystal structure of EGFR with mutant-selective dihydrodibenzodiazepinone allosteric inhibitor

PDB DOI: https://doi.org/10.2210/pdb6P1D/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-05-19 Released: 2019-12-18
Deposition Author(s): Heppner, D.E., Eck, M.J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 31749909 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.9b00381
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 152.65 kDa
Atom Count: 10,222
Modeled Residue Count: 1,196
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A [auth D], B [auth A], C [auth B], D [auth C]	327	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain F [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth D]	F [auth D], H [auth A], J [auth B], N [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth D] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth D] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C]
NQ1 (Subject of Investigation/LOI) Query on NQ1 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain E [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth D]	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		Interactions Focus chain E [auth D] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth D] Focus chain K [auth B] Focus chain M [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain G [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth D]	G [auth D], I [auth A], L [auth B], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth D] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C]

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.214 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.946	α = 90
b = 101.812	β = 101.04
c = 86.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
DIALS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Heppner, D.E.

Eck, M.J.

Funding Organization	Location	Grant 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