1TSD

THYMIDYLATE SYNTHASE COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) AND FOLATE ANALOG 1843U89

• PDB DOI: https://doi.org/10.2210/pdb1TSD/pdb

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


• Deposited: 1995-08-15 Released: 1996-01-29 
• Deposition Author(s): Weichsel, A., Montfort, W.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Observed: 0.197 

Literature

Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89.

Weichsel, A., Montfort, W.R.

(1995) Nat Struct Biol 2: 1095-1101

• PubMed: 8846221 
• DOI: https://doi.org/10.1038/nsb1295-1095
• Primary Citation of Related Structures:  
  1TSD


• PubMed Abstract: 
  

  The anticancer drug 1843U89 inhibits thymidylate synthase (TS) at sub-nanomolar concentrations and is undergoing clinical trial. The 1.95 A crystal structure of Escherichia coli TS bound to the drug and dUMP reveals that the 1843U89 binding surface includes a hydrophobic patch that is normally buried. To reach this patch, 1843U89 inserts into the wall of the TS active site, resulting in a severe local distortion of the protein. In this new conformation, active-site groups that normally bind to the catalytic cofactor methylene-tetrahydrofolate instead bind to 1843U89 in new ways. This structure provides a rare example of a protein that can bind tightly to distinct substances using a single, flexible, binding surface. This has implications for drug design, as 1843U89 could not have been obtained from current structure-based approaches.

---

Organizational Affiliation: 

Department of Biochemistry, University of Arizona Tucson 85721, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 62.86 kDa 
• Atom Count: 4,616 
• Modelled Residue Count: 530 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B	265	Escherichia coli	Mutation(s): 0  EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F89	F [auth A], H [auth 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
UMP	E [auth A], G [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UMP	Binding MOAD:  1TSD	Kd: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Observed: 0.197 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.52	α = 90
b = 127.52	β = 90
c = 68.25	γ = 120

Software Package:

Software Name	Purpose
GPRLSA	refinement
MADNES	data reduction
PROCOR	data reduction
FBSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-01-29 
Deposition Author(s): Weichsel, A., Montfort, W.R.

Revision History  

• Version 1.0: 1996-01-29
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection, Other