1SYN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 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


  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A, B
265Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
F89
Query on F89

Download SDF File 
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
FOLATE ANALOG 1843U89
C27 H24 N4 O6
BRVFNEZMTRVUGW-QFIPXVFZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FMT
Query on FMT
A, B
NON-POLYMERC H2 O2

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F89Kd: 0.1 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.346α = 90.00
b = 127.346β = 90.00
c = 68.164γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
HKLdata reduction
X-PLORrefinement
HKLdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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