6ITJ

Crystal structure of FGFR1 kinase domain in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design.

Wang, Y.Dai, Y.Wu, X.Li, F.Liu, B.Li, C.Liu, Q.Zhou, Y.Wang, B.Zhu, M.Cui, R.Tan, X.Xiong, Z.Liu, J.Tan, M.Xu, Y.Geng, M.Jiang, H.Liu, H.Ai, J.Zheng, M.

(2019) J Med Chem 62: 7473-7488

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00510
  • Primary Citation of Related Structures:  
    6ITJ, 6IUO, 6IUP

  • PubMed Abstract: 

    Alterations of fibroblast growth factor receptors (FGFRs) play key roles in numerous cancer progression and development, which makes FGFRs attractive targets in the cancer therapy. In the present study, based on a newly devised FGFR target-specific scoring function, a novel FGFR inhibitor hit was identified through virtual screening. Hit-to-lead optimization was then performed by integrating molecular docking and site-of-metabolism predictions with an array of in vitro evaluations and X-ray cocrystal structure determination, leading to a covalent FGFR inhibitor 15 , which showed a highly selective and potent FGFR inhibition profile. Pharmacokinetic assessment, protein kinase profiling, and hERG inhibition evaluation were also conducted, and they confirmed the value of 15 as a lead for further investigation. Overall, this study exemplifies the importance of the integrative use of computational methods and experimental techniques in drug discovery.


  • Organizational Affiliation

    School of Chemistry , Shanghai University , 99 ShangDa Road , Shanghai 200444 , China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 1
A, B
308Homo sapiensMutation(s): 2 
Gene Names: FGFR1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AXU
Query on AXU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-azanyl-3-(3,5-dimethyl-1-benzofuran-2-yl)-2-phenyl-6~{H}-pyrazolo[3,4-d]pyridazin-7-one
C21 H17 N5 O2
PTWNXRVSEAJTJH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AXU Binding MOAD:  6ITJ IC50: 10.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.628α = 90
b = 58.603β = 107.49
c = 65.709γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2019-10-23 
  • Deposition Author(s): Xu, Y., Liu, Q.

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description