1JG0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/s1074-5521(01)00067-9
  • Primary Citation of Related Structures:  
    1JG0

  • 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 syntha ...

    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.


    Related Citations: 
    • Structure-based discovery and in- parallel optimization of novel competitive inhibitors of thymidylate synthase
      (1999) Chem Biol 6: 319

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thymidylate synthaseAB264Escherichia coliMutation(s): 1 
Gene Names: Esherichia coli
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDT
Query on DDT

Download CCD File 
A, B
N,O-DIDANSYL-L-TYROSINE
C33 H33 N3 O7 S2
LUBOPDUYHWABFG-NDEPHWFRSA-N
 Ligand Interaction
UMP
Query on UMP

Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A,BL-PEPTIDE LINKINGC6 H11 N O4 SMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DDTKi:  1800   nM  BindingDB
DDTIC50:  5000   nM  Binding MOAD
DDTKi:  1800   nM  BindingDB
DDTIC50:  5000   nM  BindingDB
DDTIC50 :  5000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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