5NUD | pdb_00005nud

FIBROBLAST GROWTH FACTOR RECEPTOR 4 KINASE DOMAIN (449-753) IN COMPLEX WITH IRREVERSIBLE LIGAND CGA159527


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.252 (DCC) 
  • R-Value Work: 
    0.203 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5NUD

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Approaches to selective fibroblast growth factor receptor 4 inhibition through targeting the ATP-pocket middle-hinge region.

Fairhurst, R.A.Knoepfel, T.Leblanc, C.Buschmann, N.Gaul, C.Blank, J.Galuba, I.Trappe, J.Zou, C.Voshol, J.Genick, C.Brunet-Lefeuvre, P.Bitsch, F.Graus-Porta, D.Furet, P.

(2017) Medchemcomm 8: 1604-1613

  • DOI: https://doi.org/10.1039/c7md00213k
  • Primary Citation Related Structures: 
    5NUD, 5NWZ

  • PubMed Abstract: 

    A diverse range of selective FGFR4 inhibitor hit series were identified using unbiased screening approaches and by the modification of known kinase inhibitor scaffolds. In each case the origin of the selectivity was consistent with an interaction with a poorly conserved cysteine residue within the middle-hinge region of the kinase domain of FGFR4, at position 552. Targeting this region identified a non-covalent diaminopyrimidine series differentiating by size, an irreversible-covalent inhibitor in which Cys552 undergoes an SNAr reaction with a 2-chloropyridine, and a reversible-covalent inhibitor series in which Cys552 forms a hemithioacetal adduct with a 2-formyl naphthalene. In addition, the introduction of an acrylamide into a known FGFR scaffold identified a pan-FGFR inhibitor which reacted with both Cys552 and a second poorly conserved cysteine on the P-loop of FGFR4 at position 477 which is present in all four FGFR family members.


  • Organizational Affiliation
    • Novartis Institutes for BioMedical Research , CH-4002 Basel , Switzerland . Email: robin.fairhurst@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 69.37 kDa 
  • Atom Count: 4,396 
  • Modeled Residue Count: 538 
  • Deposited Residue Count: 614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 4
A, B
307Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22455
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
99K

Query on 99K



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
3-chloranyl-~{N}-(3-nitropyridin-2-yl)-5-(trifluoromethyl)pyridin-2-amine
C11 H6 Cl F3 N4 O2
OPIRLHGQOCBRTR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.252 (DCC) 
  • R-Value Work:  0.203 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.899α = 90
b = 87.054β = 90
c = 182.052γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-04-04 
  • Deposition Author(s): Zou, C.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary