4LRR

Ternary complex between E. coli thymidylate synthase, dUMP, and F9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

2'-Deoxyuridine 5'-Monophosphate Substrate Displacement in Thymidylate Synthase through 6-Hydroxy-2H-naphtho[1,8-bc]furan-2-one Derivatives.

Ferrari, S.Calo, S.Leone, R.Luciani, R.Costantino, L.Sammak, S.Di Pisa, F.Pozzi, C.Mangani, S.Costi, M.P.

(2013) J.Med.Chem. 56: 9356-9360

  • DOI: 10.1021/jm4014086

  • PubMed Abstract: 
  • Thymidylate synthase (TS) is a target for antifolate-based chemotherapies of microbial and human diseases. Here, ligand-based, synthetic, and X-ray crystallography studies led to the discovery of 6-(3-cyanobenzoyloxy)-2-oxo-2H-naphto[1,8-bc]furan, a ...

    Thymidylate synthase (TS) is a target for antifolate-based chemotherapies of microbial and human diseases. Here, ligand-based, synthetic, and X-ray crystallography studies led to the discovery of 6-(3-cyanobenzoyloxy)-2-oxo-2H-naphto[1,8-bc]furan, a novel inhibitor with a Ki of 310 nM against Pneumocystis carinii TS. The X-ray ternary complex with Escherichia coli TS revealed, for the first time, displacement of the substrate toward the dimeric protein interface, thus providing new opportunities for further design of specific inhibitors of microbial pathogens.


    Organizational Affiliation

    Department of Life Sciences, University of Modena and Reggio Emilia , Via Campi 183, 41125 Modena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A
265Escherichia coli O157:H7Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A886 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A886
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
CF9
Query on CF9

Download SDF File 
Download CCD File 
A
2-oxo-2H-naphtho[1,8-bc]furan-6-yl 4-nitrobenzoate
C18 H9 N O6
JZRRRFGHBXIXDI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CF9Ki: 6000 nM BINDINGMOAD
CF9Ki: 6000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 131.184α = 90.00
b = 131.184β = 90.00
c = 131.184γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references