Crystal structure of Escherichia coli thymidylate synthase complexed with 2'-deoxyuridine-5'-monophosphate and N,O-didansyl-L-tyrosine

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

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Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase.

Fritz, T.A.Tondi, D.Finer-Moore, J.S.Costi, M.P.Stroud, R.M.

(2001) Chem Biol 8: 981-995

  • DOI: https://doi.org/10.1016/s1074-5521(01)00067-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Protein plasticity in response to ligand binding abrogates the notion of a rigid receptor site. Thus, computational docking alone misses important prospective drug design leads. Bacterial-specific inhibitors of an essential enzyme, thymidylate synthase (TS), were developed using a combination of computer-based screening followed by in-parallel synthetic elaboration and enzyme assay [Tondi et al. (1999) Chem. Biol. 6, 319-331]. Specificity was achieved through protein plasticity and despite the very high sequence conservation of the enzyme between species. The most potent of the inhibitors synthesized, N,O-didansyl-L-tyrosine (DDT), binds to Lactobacillus casei TS (LcTS) with 35-fold higher affinity and to Escherichia coli TS (EcTS) with 24-fold higher affinity than to human TS (hTS). To reveal the molecular basis for this specificity, we have determined the crystal structure of EcTS complexed with DDT and 2'-deoxyuridine-5'-monophosphate (dUMP). The 2.0 A structure shows that DDT binds to EcTS in a conformation not predicted by molecular docking studies and substantially differently than other TS inhibitors. Binding of DDT is accompanied by large rearrangements of the protein both near and distal to the enzyme's active site with movement of C alpha carbons up to 6 A relative to other ternary complexes. This protein plasticity results in novel interactions with DDT including the formation of hydrogen bonds and van der Waals interactions to residues conserved in bacterial TS but not hTS and which are hypothesized to account for DDT's specificity. The conformation DDT adopts when bound to EcTS explains the activity of several other LcTS inhibitors synthesized in-parallel with DDT suggesting that DDT binds to the two enzymes in similar orientations. Dramatic protein rearrangements involving both main and side chain atoms play an important role in the recognition of DDT by EcTS and highlight the importance of incorporating protein plasticity in drug design. The crystal structure of the EcTS/dUMP/DDT complex is a model system to develop more selective TS inhibitors aimed at pathogenic bacterial species. The crystal structure also suggests a general formula for identifying regions of TS and other enzymes that may be treated as flexible to aid in computational methods of drug discovery.

  • Organizational Affiliation

    Macromolecular Structure Group, Department of Biochemistry, University of California San Francisco, 94143-0448, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
thymidylate synthase
A, B
264Escherichia coliMutation(s): 1 
Gene Names: Esherichia coli
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DDT

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C33 H33 N3 O7 S2
Query on UMP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C9 H13 N2 O8 P
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CXM
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
DDT BindingDB:  1JG0 Ki: min: 1800, max: 1800 (nM) from 2 assay(s)
IC50: 5000 (nM) from 1 assay(s)
Binding MOAD:  1JG0 IC50: 5000 (nM) from 1 assay(s)
PDBBind:  1JG0 IC50: 5000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.797α = 90
b = 87.062β = 90
c = 127.461γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-08
    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