1HVY

Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in the closed conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Human thymidylate synthase is in the closed conformation when complexed with dUMP and raltitrexed, an antifolate drug

Phan, J., Koli, S., Minor, W., Dunlap, R.B., Berger, S.H., Lebioda, L.

(2001) Biochemistry 40: 1897-1902


  • PubMed Abstract: 

    • Thymidylate synthase (TS) is a major target in the chemotherapy of colorectal cancer and some other neoplasms while raltitrexed (Tomudex, ZD1694) is an antifolate inhibitor of TS approved for clinical use in several European countries. The crystal st ...

    Thymidylate synthase (TS) is a major target in the chemotherapy of colorectal cancer and some other neoplasms while raltitrexed (Tomudex, ZD1694) is an antifolate inhibitor of TS approved for clinical use in several European countries. The crystal structure of the complex between recombinant human TS, dUMP, and raltitrexed has been determined at 1.9 A resolution. In contrast to the situation observed in the analogous complex of the rat TS, the enzyme is in the closed conformation and a covalent bond between the catalytic Cys 195 and dUMP is present in both subunits. This mode of ligand binding is similar to that of the analogous complex of the Escherichia coli enzyme. The only major differences observed are a direct hydrogen bond between His 196 and the O4 atom of dUMP and repositioning of the side chain of Tyr 94 by about 2 A. The thiophene ring of the drug is disordered between two parallel positions.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 92908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A, B, C, D
288Homo sapiensMutation(s): 0 
Gene Names: TYMS (TS)
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Go to Gene View: TYMS
Go to UniProtKB:  P04818
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D16
Query on D16
Download SDF File 
Download CCD File 
A, B, C, D
TOMUDEX
ZD1694; Raltitrexed
C21 H22 N4 O6 S
IVTVGDXNLFLDRM-HNNXBMFYSA-N
 Ligand Interaction
BME
Query on BME
Download SDF File 
Download CCD File 
A, B, C, D
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
UMP
Query on UMP
Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D16IC50: 290 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 68.849α = 70.23
b = 70.495β = 83.29
c = 74.533γ = 73.28
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-10-10
    Type: Non-polymer description
  • Version 1.4: 2017-10-04
    Type: Refinement description