6LVL

Crystal structure of FGFR2 in complex with 1,3,5-triazine derivative

• PDB DOI:  https://doi.org/10.2210/pdb6LVL/pdb

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


• Deposited: 2020-02-04 Released: 2020-04-08 
• Deposition Author(s): Echizen, Y., Tateishi, Y., Amano, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structure-based drug design of 1,3,5-triazine and pyrimidine derivatives as novel FGFR3 inhibitors with high selectivity over VEGFR2.

Kuriwaki, I., Kameda, M., Hisamichi, H., Kikuchi, S., Iikubo, K., Kawamoto, Y., Moritomo, H., Kondoh, Y., Amano, Y., Tateishi, Y., Echizen, Y., Iwai, Y., Noda, A., Tomiyama, H., Suzuki, T., Hirano, M.

(2020) Bioorg Med Chem 28: 115453-115453

• PubMed: 32278710 
• DOI: https://doi.org/10.1016/j.bmc.2020.115453
• Primary Citation of Related Structures:  
  6LVK, 6LVL, 6LVM


• PubMed Abstract: 
  

Fibroblast growth factor receptor 3 (FGFR3) is an attractive therapeutic target for the treatment of bladder cancer. We identified 1,3,5-triazine derivative 18b and pyrimidine derivative 40a as novel structures with potent and highly selective FGFR3 inhibitory activity over vascular endothelial growth factor receptor 2 (VEGFR2) using a structure-based drug design (SBDD) approach. X-ray crystal structure analysis suggests that interactions between 18b and amino acid residues located in the solvent region (Lys476 and Met488), and between 40a and Met529 located in the back pocket of FGFR3 may underlie the potent FGFR3 inhibitory activity and high kinase selectivity over VEGFR2.

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Organizational Affiliation: 

Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.

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: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.16 kDa 
• Atom Count: 4,678 
• Modelled Residue Count: 574 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 2	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: FGFR2, BEK, KGFR, KSAM EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens) Explore P21802  Go to UniProtKB:  P21802
PHAROS:  P21802

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVL (Subject of Investigation/LOI)	D [auth A], H [auth B]	N-ethyl-2-[[4-[[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]-1,3,5-triazin-2-yl]amino]benzenesulfonamide C28 H39 N9 O3 S YJUANBRSJHPDHJ-UHFFFAOYSA-N
SO4	C [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.251 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.675	α = 90
b = 116.136	β = 90
c = 64.202	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Echizen, Y., Tateishi, Y., Amano, Y.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-29
  Changes: Database references