4ZSA

Crystal structure of FGFR1 kinase domain in complex with 7n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, synthesis and biological evaluation of novel FGFR inhibitors bearing an indazole scaffold.

Liu, J.Peng, X.Dai, Y.Zhang, W.Ren, S.Ai, J.Geng, M.Li, Y.

(2015) Org.Biomol.Chem. 13: 7643-7654

  • DOI: 10.1039/c5ob00778j

  • PubMed Abstract: 
  • Fibroblast growth factor receptor (FGFR) is a potential target for cancer therapy. Based on the structure of AZD4547 and NVPBGJ-398, we designed novel 1H-indazol-3-amine scaffold derivatives by utilizing scaffold hopping and molecular hybridization s ...

    Fibroblast growth factor receptor (FGFR) is a potential target for cancer therapy. Based on the structure of AZD4547 and NVPBGJ-398, we designed novel 1H-indazol-3-amine scaffold derivatives by utilizing scaffold hopping and molecular hybridization strategies. Consequently, twenty-eight new compounds were synthesized and evaluated for their inhibitory activity against FGFR1. Compound 7n bearing a 6-(3-methoxyphenyl)-1H-indazol-3-amine scaffold was first identified as a potent FGFR1 inhibitor, with good enzymatic inhibition (IC50 = 15.0 nM) and modest cellular inhibition (IC50 = 642.1 nM). The crystal structure of 7n bound to FGFR1 was obtained, which might provide a new basis for potent inhibitor design. Further structural optimization revealed that compound 7r stood out as the most potent FGFR1 inhibitor with the best enzyme inhibitory (IC50 = 2.9 nM) and cellular activity (IC50 = 40.5 nM).


    Organizational Affiliation

    School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China. liyx417@fudan.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibroblast growth factor receptor 1
A, B
308Homo sapiensMutation(s): 2 
Gene Names: FGFR1 (BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR)
EC: 2.7.10.1
Find proteins for P11362 (Homo sapiens)
Go to Gene View: FGFR1
Go to UniProtKB:  P11362
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4UT
Query on 4UT

Download SDF File 
Download CCD File 
A, B
4-(4-ethylpiperazin-1-yl)-N-[6-(3-methoxyphenyl)-2H-indazol-3-yl]benzamide
C27 H29 N5 O2
LDEZCHXBGZHBFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 209.910α = 90.00
b = 57.181β = 107.47
c = 65.550γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-05-13 
  • Released Date: 2015-06-17 
  • Deposition Author(s): Liu, Q.F., Xu, Y.C.

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references