9DF2 | pdb_00009df2

EGFR Exon20 insertion mutant ASV bound with (S)-3-((3-chloro-2-methoxyphenyl)amino)-2-(3-((tetrahydrofuran-2-yl)methoxy)pyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.245 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

STX-721, a Covalent EGFR/HER2 Exon 20 Inhibitor, Utilizes Exon 20-Mutant Dynamic Protein States and Achieves Unique Mutant Selectivity Across Human Cancer Models.

Pagliarini, R.A.Henderson, J.A.Milgram, B.C.Borrelli, D.R.Brooijmans, N.Hilbert, B.J.Huff, M.R.Ito, T.Kryukov, G.V.Ladd, B.Martin, B.R.Motiwala, H.O'Hearn, E.Tsai, C.F.Wang, W.Bellier, J.Boland, L.Clark, S.Hensley, E.Hata, A.N.Kuzmic, P.Guzman-Perez, A.Jackson, E.L.Stuart, D.D.

(2025) Clin Cancer Res 31: 3002-3018

  • DOI: https://doi.org/10.1158/1078-0432.CCR-24-3833
  • Primary Citation of Related Structures:  
    9DF2, 9DF3, 9DF4, 9GI9, 9GL7, 9GL8, 9GL9

  • PubMed Abstract: 

    Commonly occurring oncogenic mutations in EGFR render non-small cell lung cancers sensitive to approved EGFR-targeted drugs. EGFR in-frame exon 20 insertion (ex20ins) mutants are, however, less sensitive to such drugs. The efficacy of existing medicines may in part be limited by their selectivity for ex20ins mutations relative to wild-type EGFR, which is important for epithelial tissue homeostasis. We solved high-resolution crystal structures of clinically frequent ex20ins mutants to better understand how to achieve mutant-selective inhibition. Analyses of these structures demonstrate targetable ex20ins-mutant-biased dynamic protein states. To exploit these findings, we designed STX-721, an irreversible EGFR/ERBB2 ex20ins-mutant-selective inhibitor, and characterized its activity relative to clinical phase benchmarks across multiple preclinical assays. Structural analyses predict that STX-721 takes advantage of ex20ins-mutant-selective dynamic states. In carefully benchmarked biochemical, biophysical, and cellular assays, STX-721 demonstrated superior ex20ins-mutant selectivity relative to other tested benchmark clinical phase compounds and achieved ex20ins-mutant-selective tumor regression in vivo. These data highlight that STX-721 shows a high level of mutant EGFR selectivity across human preclinical cancer models and may provide an improved clinical efficacy versus adverse event profile relative to existing drugs.


  • Organizational Affiliation
    • Scorpion Therapeutics, Boston, Massachusetts.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor333Homo sapiensMutation(s): 1 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IMS (Subject of Investigation/LOI)
Query on A1IMS

Download Ideal Coordinates CCD File 
B [auth A]3-[(3-chloranyl-2-methoxy-phenyl)amino]-2-[3-[[(2S)-oxolan-2-yl]methoxy]pyridin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one
C24 H25 Cl N4 O4
FDWHIPNBDNBCNI-CQSZACIVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
N [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.07α = 90
b = 106.9β = 90
c = 176.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 1.2: 2025-07-23
    Changes: Database references