1F4G

CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH SP-876


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Site-directed ligand discovery.

Erlanson, D.A.Braisted, A.C.Raphael, D.R.Randal, M.Stroud, R.M.Gordon, E.M.Wells, J.A.

(2000) Proc Natl Acad Sci U S A 97: 9367-9372

  • DOI: https://doi.org/10.1073/pnas.97.17.9367
  • Primary Citation of Related Structures:  
    1F4B, 1F4C, 1F4D, 1F4E, 1F4F, 1F4G

  • PubMed Abstract: 

    We report a strategy (called "tethering") to discover low molecular weight ligands ( approximately 250 Da) that bind weakly to targeted sites on proteins through an intermediary disulfide tether. A native or engineered cysteine in a protein is allowed to react reversibly with a small library of disulfide-containing molecules ( approximately 1,200 compounds) at concentrations typically used in drug screening (10 to 200 microM). The cysteine-captured ligands, which are readily identified by MS, are among the most stable complexes, even though in the absence of the covalent tether the ligands may bind very weakly. This method was applied to generate a potent inhibitor for thymidylate synthase, an essential enzyme in pyrimidine metabolism with therapeutic applications in cancer and infectious diseases. The affinity of the untethered ligand (K(i) approximately 1 mM) was improved 3,000-fold by synthesis of a small set of analogs with the aid of crystallographic structures of the tethered complex. Such site-directed ligand discovery allows one to nucleate drug design from a spatially targeted lead fragment.


  • Organizational Affiliation

    Sunesis Pharmaceuticals, Incorporated, Redwood City, CA 94063, USA. erlanson@sunesis-pharma.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDYLATE SYNTHASE
A, B
264Escherichia coliMutation(s): 2 
EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A884
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A, B
L-PEPTIDE LINKINGC6 H11 N O4 SMET
MHO
Query on MHO
A, B
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Binding Affinity Annotations 
IDSourceBinding Affinity
TP4 PDBBind:  1F4G Ki: 330 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.03α = 90
b = 126.03β = 90
c = 66.84γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2018-02-28
    Changes: Experimental preparation
  • Version 1.6: 2021-11-03
    Changes: Database references, Derived calculations