9UHI | pdb_00009uhi

FGFR1 kinase domain with a covalent inhibitor 9o


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.197 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Design, Synthesis and Biological Evaluation of 7-(1-Methyl-1 H -indole-3-yl)-5 H -pyrrolo[2,3- b ]pyrazine Derivatives as Novel Covalent pan-FGFR Inhibitors to Overcome Clinical Resistance.

Deng, W.Chen, X.Yan, L.Xiang, S.Song, X.Zhang, L.Li, X.Zhu, W.Pei, J.Lin, X.Patterson, A.V.Smaill, J.B.Li, B.Tu, Z.Zhou, Y.Chen, Y.Lu, X.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01594
  • Primary Citation of Related Structures:  
    9UHC, 9UHI

  • PubMed Abstract: 

    Aberrant activation of fibroblast growth factor receptors (FGFRs) plays a critical role in tumorigenesis across multiple cancer types, driving the development of various FGFR inhibitors. Despite clinical advances, therapeutic efficacy remains limited by the emergence of drug resistance, primarily mediated by gatekeeper mutations in FGFRs. To overcome this challenge, we designed and synthesized a novel series of 7-(1-methyl-1 H -indole-3-yl)-5 H -pyrrolo[2,3- b ]pyrazine derivatives as covalent pan-FGFR inhibitors targeting both wild-type and gatekeeper mutants. Compound 9p demonstrated potent nanomolar inhibitory activity against FGFR1-3 and gatekeeper mutants in biochemical and cellular assays. Structural characterization using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) and X-ray crystallography confirmed covalent binding of 9p to FGFR1. Additionally, 9p showed significant in vivo antitumor efficacy in nude mice bearing the RT112 bladder cancer xenograft model. These findings establish 9p as a promising lead for further development of FGFR-targeted anticancer therapies.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 1
A, B
310Homo sapiensMutation(s): 0 
Gene Names: FGFR1BFGFRCEKFGFBRFLGFLT2HBGFR
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
PHAROS:  P11362
GTEx:  ENSG00000077782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11362
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EPF (Subject of Investigation/LOI)
Query on A1EPF

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
~{N}-[1-methyl-3-[3-[1-(2-morpholin-4-ylethyl)pyrazol-4-yl]quinoxalin-5-yl]indol-6-yl]propanamide
C29 H31 N7 O2
MZNNPOZDHTXUDT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.197 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.43α = 90
b = 49.28β = 107.42
c = 66.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82202920
National Natural Science Foundation of China (NSFC)China82172654

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release