5O4A

Human FGF in complex with a covalent inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

A study of the reactivity of S(VI)-F containing warheads with nucleophilic amino-acid side chains under physiological conditions.

Mukherjee, H., Debreczeni, J., Breed, J., Tentarelli, S., Aquila, B., Dowling, J.E., Whitty, A., Grimster, N.P.

(2017) Org. Biomol. Chem. 15: 9685-9695

  • DOI: 10.1039/c7ob02028g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Sulfonyl fluorides (SFs) have recently emerged as a promising warhead for the targeted covalent modification of proteins. Despite numerous examples of the successful deployment of SFs as covalent probe compounds, a detailed exploration of the factors ...

    Sulfonyl fluorides (SFs) have recently emerged as a promising warhead for the targeted covalent modification of proteins. Despite numerous examples of the successful deployment of SFs as covalent probe compounds, a detailed exploration of the factors influencing the stability and reactivity of SFs has not yet appeared. In this work we present an extensive study on the influence of steric and electronic factors on the reactivity and stability of the SF and related SVI-F groups. While SFs react rapidly with N-acetylcysteine, the resulting adducts were found to be unstable, rendering SFs inappropriate for the durable covalent inhibition of cysteine residues. In contrast, SFs afforded stable adducts with both N-acetyltyrosine and N-acetyllysine; furthermore, we show that the reactivity of arylsulfonyl fluorides towards these nucleophilic amino acids can be predictably modulated by adjusting the electronic properties of the warhead. These trends were largely conserved when the covalent reaction occurred within a protein binding pocket. We have also obtained a crystal structure depicting covalent modification of the catalytic lysine of a tyrosine kinase (FGFR1) by the ATP analog 5'-O-3-((fluorosulfonyl)benzoyl)adenosine (m-FSBA). Highly reactive warheads were demonstrated to be unstable with respect to hydrolysis in buffered aqueous solutions, indicating that warhead reactivity must be carefully tuned to provide optimal rates of protein modification. Our results demonstrate that the reactivity of SFs complements that of more commonly studied acrylamides, and we hope that this work spurs the rational design of novel SF-containing covalent probe compounds and inhibitors, particularly in cases where a suitably positioned cysteine residue is not present.

    Organizational Affiliation: 

    IMED Oncology, AstraZeneca, Waltham, Massachusetts 02451, USA. neil.grimster@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibroblast growth factor receptor 1
A, B
309Homo sapiensMutation(s): 0 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
9K8
Query on 9K8
Download SDF File 
Download CCD File 
A, B
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 4-ethyl-3-fluorosulfonyl-benzoate
C19 H20 F N5 O7 S
BSCRHVZAWVIUPR-XKLVTHTNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 211.140α = 90.00
b = 57.270β = 107.57
c = 66.800γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release