6JPJ | pdb_00006jpj

Crystal structure of FGF401 in complex of FGFR4

• PDB DOI: https://doi.org/10.2210/pdb6JPJ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-03-27 Released: 2019-05-15 
• Deposition Author(s): Zhou, Z., Chen, X., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.243 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Characterization of FGF401 as a reversible covalent inhibitor of fibroblast growth factor receptor 4.

Zhou, Z., Chen, X., Fu, Y., Zhang, Y., Dai, S., Li, J., Chen, L., Xu, G., Chen, Z., Chen, Y.

(2019) Chem Commun (Camb) 55: 5890-5893

• PubMed: 31041948 
• DOI: https://doi.org/10.1039/c9cc02052g
• Primary Citation of Related Structures:  
  6JPJ


• PubMed Abstract: 
  

  Biochemical and structural studies provide information on the mode of action of FGF401 as a selective, reversible covalent inhibitor of FGFR4. Kinase and proliferation assays reveal that FGF401 has the ability to overcome gatekeeper mutations in FGFR4.

---

Organizational Affiliation: 

NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 35.36 kDa 
• Atom Count: 2,444 
• Modelled Residue Count: 299 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A	311	Homo sapiens	Mutation(s): 2  Gene Names: FGFR4, JTK2, TKF EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P22455 (Homo sapiens) Explore P22455  Go to UniProtKB:  P22455
PHAROS:  P22455 GTEx:  ENSG00000160867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FGF (Subject of Investigation/LOI)	B [auth A]	N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide C25 H30 N8 O4 BHKDKKZMPODMIQ-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
FGF	BindingDB:  6JPJ	IC50: min: 1.3, max: 12 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.243 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.275	α = 90
b = 60.931	β = 98.56
c = 61.154	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Zhou, Z., Chen, X., Chen, Y.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81372904, 81570537, 81272971

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-16
  Changes: Structure summary