Human Thymidylate Synthase Bound to dUMP and LY231514, a Pyrrolo(2,3-d)pyrimidine-based Antifolate

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.273 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases.

Sayre, P.H.Finer-Moore, J.S.Fritz, T.A.Biermann, D.Gates, S.B.MacKellar, W.C.Patel, V.F.Stroud, R.M.

(2001) J Mol Biol 313: 813-829

  • DOI: https://doi.org/10.1006/jmbi.2001.5074
  • Primary Citation of Related Structures:  
    1JTQ, 1JTU, 1JU6, 1JUJ, 1JUT

  • PubMed Abstract: 

    Crystal structures of four pyrrolo(2,3-d)pyrimidine-based antifolate compounds, developed as inhibitors of thymidylate synthase (TS) in a strategy to circumvent drug-resistance, have been determined in complexes with their in vivo target, human thymidylate synthase, and with the structurally best-characterized Escherichia coli enzyme, to resolutions of 2.2-3.0 A. The 2.9 A crystal structure of a complex of human TS with one of the inhibitors, the multi-targeted antifolate LY231514, demonstrates that this compound induces a "closed" enzyme conformation and leads to formation of a covalent bond between enzyme and substrate. This structure is one of the first liganded human TS structures, and its solution was aided by mutation to facilitate crystallization. Structures of three other pyrrolo(2,3-d)pyrimidine-based antifolates in complex with Escherichia coli TS confirm the orientation of this class of inhibitors in the active site. Specific interactions between the polyglutamyl moiety and a positively charged groove on the enzyme surface explain the marked increase in affinity of the pyrrolo(2,3-d)pyrimidine inhibitors once they are polyglutamylated, as mediated in vivo by the cellular enzyme folyl polyglutamate synthetase.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143-0448, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
313Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
GTEx:  ENSG00000176890 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04818
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LYA PDBBind:  1JUJ Ki: 109 (nM) from 1 assay(s)
BindingDB:  1JUJ Ki: min: 1.3, max: 340 (nM) from 3 assay(s)
IC50: min: 70, max: 1.10e+5 (nM) from 9 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.14α = 90
b = 98.14β = 110.7
c = 111.97γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description