7F3M | pdb_00007f3m

Crystal structure of FGFR4 kinase domain with PRN1371

• PDB DOI: https://doi.org/10.2210/pdb7F3M/pdb

• Classification: TRANSFERASE-TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2021-06-16 Released: 2022-01-12 
• Deposition Author(s): Chen, X.J., Qu, L.Z., Dai, S.Y., Wei, H.D., Chen, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors

Qu, L., Chen, X., Wei, H., Guo, M., Dai, S., Jiang, L., Li, J., Yue, S., Chen, Z., Chen, Y.

(2022) Commun Chem 5: 5

• DOI: https://doi.org/10.1038/s42004-021-00623-x

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: 35.54 kDa 
• Atom Count: 2,545 
• Modeled Residue Count: 298 
• 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): 1  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
GX3 (Subject of Investigation/LOI)	B [auth A]	6-[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]-2-(methylamino)-8-[3-(4-prop-2-enoylpiperazin-1-yl)propyl]pyrido[2,3-d]pyrimidin-7-one C26 H30 Cl2 N6 O4 PUIXMSRTTHLNKI-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
GX3	BindingDB:  7F3M	Ki: 73 (nM) from 1 assay(s)
		IC50: 19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.449	α = 90
b = 61.1	β = 97.65
c = 61.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Chen, X.J., Qu, L.Z., Dai, S.Y., Wei, H.D., Chen, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81570537
National Natural Science Foundation of China (NSFC)	China	81974074
National Natural Science Foundation of China (NSFC)	China	31900880

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2022-01-26
  Changes: Database references
• Version 1.2: 2022-03-09
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description