The crystal structure of FGFR4 kinase domain in complex with LY2874455

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 

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Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455

Wu, D.Guo, M.Philips, M.A.Qu, L.Jiang, L.Li, J.Chen, X.Chen, Z.Chen, L.Chen, Y.

(2016) PLoS One 11: e0162491-e0162491

  • DOI: https://doi.org/10.1371/journal.pone.0162491
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

  • Organizational Affiliation

    Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4311Homo sapiensMutation(s): 0 
Gene Names: FGFR4JTK2TKF
UniProt & NIH Common Fund Data Resources
Find proteins for P22455 (Homo sapiens)
Explore P22455 
Go to UniProtKB:  P22455
PHAROS:  P22455
GTEx:  ENSG00000160867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22455
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6LF

Download Ideal Coordinates CCD File 
B [auth A]2-[4-[E-2-[5-[(1R)-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1H-indazol-3-yl]ethenyl]pyrazol-1-yl]ethanol
C21 H19 Cl2 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
6LF Binding MOAD:  5JKG IC50: 6.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.887α = 90
b = 61.887β = 90
c = 186.059γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81372904
National Natural Science Foundation of ChinaChina81570537
National Natural Science Foundation of ChinaChina81272971

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations