1JU6

Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases.

Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M.

(2001) J Mol Biol 313: 813-829

  • DOI: 10.1006/jmbi.2001.5074
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Crystal structures of four pyrrolo(2,3-d)pyrimidine-based antifolate compounds, developed as inhibitors of thymidylate synthase (TS) in a strategy to circumvent drug-resistance, have been determined in complexes with their in vivo target, human thymi ...

    Crystal structures of four pyrrolo(2,3-d)pyrimidine-based antifolate compounds, developed as inhibitors of thymidylate synthase (TS) in a strategy to circumvent drug-resistance, have been determined in complexes with their in vivo target, human thymidylate synthase, and with the structurally best-characterized Escherichia coli enzyme, to resolutions of 2.2-3.0 A. The 2.9 A crystal structure of a complex of human TS with one of the inhibitors, the multi-targeted antifolate LY231514, demonstrates that this compound induces a "closed" enzyme conformation and leads to formation of a covalent bond between enzyme and substrate. This structure is one of the first liganded human TS structures, and its solution was aided by mutation to facilitate crystallization. Structures of three other pyrrolo(2,3-d)pyrimidine-based antifolates in complex with Escherichia coli TS confirm the orientation of this class of inhibitors in the active site. Specific interactions between the polyglutamyl moiety and a positively charged groove on the enzyme surface explain the marked increase in affinity of the pyrrolo(2,3-d)pyrimidine inhibitors once they are polyglutamylated, as mediated in vivo by the cellular enzyme folyl polyglutamate synthetase.

    Related Citations: 
    • Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site
      Schiffer, C.A., Clifton, I.J., Davisson, V.J., Santi, D.V., Stroud, R.M.
      (1995) Biochemistry 34: 16279
    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A, B, C, D
313Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS  P04818
GTEx  ENSG00000176890
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYA
Query on LYA
Download CCD File 
A, B, C, D
2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID
C20 H21 N5 O6
WBXPDJSOTKVWSJ-ZDUSSCGKSA-N		 Ligand Interaction
UMP
Query on UMP
Download CCD File 
A, B, C, D
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LYAKi:  1.2999999523162842   nM  BindingDB
LYAIC50:  20000   nM  BindingDB
LYAKi:  340   nM  BindingDB
LYAKi:  340   nM  BindingDB
LYAIC50:  5700   nM  BindingDB
LYAIC50:  11000   nM  BindingDB
LYAIC50:  20000   nM  BindingDB
LYAIC50:  9500   nM  BindingDB
LYAIC50:  19000   nM  BindingDB
LYAIC50:  29000   nM  BindingDB
LYAIC50:  110000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.138α = 71.67
b = 69.633β = 85.72
c = 73.958γ = 75.11
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance