Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 37.16 kDa 
• Atom Count: 2941 
• Residue Count: 316 
• Unique protein chains: 1

1TSL

L. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR

• DOI: 10.2210/pdb1TSL/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Lacticaseibacillus casei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-06-12 Released: 1998-06-17 
• Deposition Author(s): Stout, T.J., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Literature

Structure-based design of inhibitors specific for bacterial thymidylate synthase.

Stout, T.J., Tondi, D., Rinaldi, M., Barlocco, D., Pecorari, P., Santi, D.V., Kuntz, I.D., Stroud, R.M., Shoichet, B.K., Costi, M.P.

(1999) Biochemistry 38: 1607-1617

• PubMed: 9931028 
• DOI: 10.1021/bi9815896
• Primary Citation of Related Structures:  
  1TSM, 1TSL


• PubMed Abstract: 
  

Thymidylate synthase is an attractive target for antiproliferative drug design because of its key role in the synthesis of DNA. As such, the enzyme has been widely targeted for anticancer applications. In principle, TS should also be a good target for drugs used to fight infectious disease. In practice, TS is highly conserved across species, and it has proven to be difficult to develop inhibitors that are selective for microbial TS enzymes over the human enzyme. Using the structure of TS from Lactobacillus casei in complex with the nonsubstrate analogue phenolphthalein, inhibitors were designed to take advantage of features of the bacterial enzyme that differ from those of the human enzyme. Upon synthesis and testing, these inhibitors were found to be up to 40-fold selective for the bacterial enzyme over the human enzyme. The crystal structures of two of these inhibitors in complex with TS suggested the design of further compounds. Subsequent synthesis and testing showed that these second-round compounds inhibit the bacterial enzyme at sub-micromolar concentrations, while the human enzyme was not inhibited at detectable levels (selectivities of 100-1000-fold or greater). Although these inhibitors share chemical similarities, X-ray crystal structures reveal that the analogues bind to the enzyme in substantially different orientations. Site-directed mutagenesis experiments suggest that the individual inhibitors may adopt multiple configurations in their complexes with TS.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A	316	Lacticaseibacillus casei	Mutation(s): 0  Gene Names: thyA EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei) Explore P00469  Go to UniProtKB:  P00469

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A15	A	3'-3"-DICHLOROPHENOL-1,8-3H-BENZO[DE]ISOCHROMEN-1-ONE C24 H14 Cl2 O4 HCQHFJBXXMFZHF-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
A15	Ki:  700   nM  BindingDB
A15	Ki:  700   nM  Binding MOAD
A15	Ki :  700   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.3	α = 90
b = 78.3	β = 90
c = 243.2	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MSC	data reduction
MSC	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-06-12 
• Released Date: 1998-06-17 
Deposition Author(s): Stout, T.J., Stroud, R.M.

Revision History 

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance