7VJL | pdb_00007vjl

The crystal structure of FGFR4 kinase domain in complex with N-(5-cyano-4-((2-methoxyethyl)amino)pyridin-2-yl)-7-(2,2,2-trifluoroacetyl)-3,4-dihydro-1,8-naphthyridine-1(2H)-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb7VJL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia alba
• Mutation(s): No 


• Deposited: 2021-09-28 Released: 2022-02-23 
• Deposition Author(s): Zhang, Z.M., Wang, Y.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Characterization of an aromatic trifluoromethyl ketone as a new warhead for covalently reversible kinase inhibitor design.

Zhang, Z., Wang, Y., Chen, X., Song, X., Tu, Z., Chen, Y., Zhang, Z., Ding, K.

(2021) Bioorg Med Chem 50: 116457-116457

• PubMed: 34670167 
• DOI: https://doi.org/10.1016/j.bmc.2021.116457
• Primary Citation Related Structures: 
  7VJL


• PubMed Abstract: 
  

  An aromatic trifluoromethyl ketone moiety was characterized as a new warhead for covalently reversible kinase inhibitor design to target the non-catalytic cysteine residue. Potent and selective covalently reversible inhibitors of FGFR4 kinase were successfully designed and synthesized by utilizing this new warhead. The binding mode of a representative inhibitor was fully characterized by using multiple technologies including MALDI-TOF mass spectrometry, dialysis assay and X-ray crystallographic studies etc. This functional group was also successfully applied to discovery of a new JAK3 inhibitor, suggesting its potential application in designing other kinase inhibitors.

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Organizational Affiliation: 
• International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China.
International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China.
International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; The First Affiliated Hospital, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.51 kDa 
• Atom Count: 4,186 
• Modeled Residue Count: 529 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A, B	301	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7IF (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[5-(aminomethyl)-4-(2-methoxyethylamino)pyridin-2-yl]-7-[2,2,2-tris(fluoranyl)ethanoyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide C20 H23 F3 N6 O3 OEKVHZLDKRFXOH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.37	α = 90
b = 66.785	β = 90
c = 184.174	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
Coot	model building
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Zhang, Z.M., Wang, Y.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 2.0: 2022-05-04
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-09-07
  Changes: Database references
• Version 2.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-13
  Changes: Structure summary