1SYN

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH BW1843U89 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition.

Stout, T.J.Stroud, R.M.

(1996) Structure 4: 67-77

  • DOI: 10.1016/s0969-2126(96)00010-x
  • Primary Citation of Related Structures:  
    1SYN

  • PubMed Abstract: 
  • Thymidylate synthase (TS) is critical to DNA synthesis as it catalyzes the rate limiting step in the only biosynthetic pathway for deoxythymidine monophosphate (dTMP) production. TS is therefore an important target for anti-proliferative and anti-can ...

    Thymidylate synthase (TS) is critical to DNA synthesis as it catalyzes the rate limiting step in the only biosynthetic pathway for deoxythymidine monophosphate (dTMP) production. TS is therefore an important target for anti-proliferative and anti-cancer drug design. The TS enzymatic mechanism involves the reductive methylation of the substrate, deoxyuridine monophosphate (dUMP), by transfer of a methylene group from the co-factor, methylenetetrahydrofolate (CH2H4folate), resulting in the production of deoxythymidine monophosphate (dTMP) and dihydrofolate (H2folate). Previous drug design efforts based on co-factor analogues have produced good inhibitors of TS, but poor bioavailability and toxicity have limited their usefulness. BW1843U89, a folate analogue, is a recently developed compound which is an exceptionally strong inhibitor (Ki = 0.09 nM), has good bioavailability and in clinical trials thus far has not demonstrated significant toxicity.


    Related Citations: 
    • Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
      Montfort, W.R., Perry, K.M., Fauman, E.B., Finer-Moore, J.S., Maley, G.F., Hardy, L., Maley, F., Stroud, R.M.
      (1990) Biochemistry 29: 6964

    Organizational Affiliation

    Department of Biochemistry and Biophysics, School of Medicine, University of California at San Francisco 94143-0448, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDYLATE SYNTHASEA, B265Escherichia coliMutation(s): 0 
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
F89
Query on F89

Download CCD File 
A, B
S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
C27 H24 N4 O6
BRVFNEZMTRVUGW-QFIPXVFZSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F89Kd:  0.10000000149011612   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.346α = 90
b = 127.346β = 90
c = 68.164γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
HKLdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance