7DHL

Crystal structure of FGFR3 in complex with pyrimidine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Synthesis and structure-activity relationships of pyrimidine derivatives as potent and orally active FGFR3 inhibitors with both increased systemic exposure and enhanced in vitro potency.

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

(2021) Bioorg Med Chem 33: 116019-116019

  • DOI: 10.1016/j.bmc.2021.116019
  • Primary Citation of Related Structures:  
    7DHL

  • PubMed Abstract: 
  • Fibroblast growth factor receptor 3 (FGFR3) is an attractive therapeutic target for the treatment of patients with bladder cancer harboring genetic alterations in FGFR3. We identified pyrimidine derivative 20b, which induced tumor regression following oral administration to a bladder cancer xenograft mouse model ...

    Fibroblast growth factor receptor 3 (FGFR3) is an attractive therapeutic target for the treatment of patients with bladder cancer harboring genetic alterations in FGFR3. We identified pyrimidine derivative 20b, which induced tumor regression following oral administration to a bladder cancer xenograft mouse model. Compound 20b was discovered by optimizing lead compound 1, which we reported previously. Specifically, reducing the molecular size of the substituent at the 4-position and replacing the linker of the 5-position in the pyrimidine scaffold resulted in an increase in systemic exposure. Furthermore, introduction of two fluorine atoms into the 3,5-dimethoxyphenyl ring enhanced FGFR3 inhibitory activity. Molecular dynamics (MD) simulation of 20b suggested that the fluorine atom interacts with the main chain NH moiety of Asp635 via a hydrogen bond.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 3A313Homo sapiensMutation(s): 0 
Gene Names: FGFR3JTK4
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P22607 (Homo sapiens)
Explore P22607 
Go to UniProtKB:  P22607
PHAROS:  P22607
GTEx:  ENSG00000068078 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22607
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H6X (Subject of Investigation/LOI)
Query on H6X

Download Ideal Coordinates CCD File 
B [auth A]5-[2-(3,5-dimethoxyphenyl)ethyl]-N-[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]pyrimidin-2-amine
C31 H42 N6 O3
KTAFHTVOQVOCCA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.14α = 90
b = 61.4β = 112.88
c = 59.895γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release