7DTZ | pdb_00007dtz

FGFR4 complex with a covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7DTZ/pdb

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


• Deposited: 2021-01-07 Released: 2021-04-14 
• Deposition Author(s): Chen, X.J., Dai, S.Y., Chen, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Investigation of Covalent Warheads in the Design of 2-Aminopyrimidine-based FGFR4 Inhibitors.

Deng, W., Chen, X., Jiang, K., Song, X., Huang, M., Tu, Z.C., Zhang, Z., Lin, X., Ortega, R., Patterson, A.V., Smaill, J.B., Ding, K., Chen, S., Chen, Y., Lu, X.

(2021) ACS Med Chem Lett 12: 647-652

• PubMed: 33859803 
• DOI: https://doi.org/10.1021/acsmedchemlett.1c00052
• Primary Citation Related Structures: 
  7DTZ


• PubMed Abstract: 
  

  Covalent kinase inhibitors are rapidly emerging as a class of therapeutics with clinical benefits. Herein we report a series of selective 2-aminopyrimidine-based fibroblast growth factor receptor 4 (FGFR4) inhibitors exploring different types of cysteine-targeting warheads. The structure-activity relationship study revealed that the chemically tuned warheads α-fluoro acrylamide, vinylsulfonamide, and acetaldehyde amine were suitable as covalent warheads for the design of selective FGFR4 inhibitors. Compounds 6a , 6h , and 6i selectively suppressed FGFR4 enzymatic activity with IC ₅₀ values of 53 ± 18, 45 ± 11, and 16 ± 4 nM, respectively, while sparing FGFR1/2/3. X-ray crystal structure and MALDI-TOF studies demonstrated that compound 6h bearing the α-fluoro acrylamide binds to FGFR4 with an irreversible binding mode, whereas compound 6i with an acetaldehyde amine binds to FGFR4 with a reversible covalent mode. 6h and 6i might provide some fundamental structural information for the rational design of new selective FGFR4 inhibitors.

---

Organizational Affiliation: 
• School of Pharmacy, Jinan University, #601 Huangpu Avenue West, Guangzhou 510632, China.
Department of Oncology, NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190 Kaiyuan Avenue, Guangzhou 510530, China.
Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
Yancheng Dafeng People's Hospital, #139 Xingfu East Road, Dafeng District,Yancheng 224100, China.

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: 35.11 kDa 
• Atom Count: 2,721 
• Modeled Residue Count: 299 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A	309	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
HHL (Subject of Investigation/LOI)	B [auth A]	N-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide C23 H21 Cl2 F N4 O4 GRLPJXHTSUIFNY-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
HHL	BindingDB:  7DTZ	IC50: min: 45, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.182	α = 90
b = 61.434	β = 97.65
c = 60.504	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Chen, X.J., Dai, S.Y., Chen, Y.H.

---

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

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2021-04-28
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary