1JUJ

Human Thymidylate Synthase Bound to dUMP and LY231514, a Pyrrolo(2,3-d)pyrimidine-based Antifolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.273 

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Ligand Structure Quality Assessment 


This is version 1.3 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
  • Primary Citation of Related Structures:  
    1JTQ, 1JTU, 1JU6, 1JUJ, 1JUT

  • 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 thymidylate synthase, and with the structurally best-characterized Escherichia coli enzyme, to resolutions of 2 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDYLATE SYNTHASEA, B, C, D313Homo sapiensMutation(s): 1 
Gene Names: TYMSTSOK/SW-cl.29
EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
PHAROS:  P04818
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYA (Subject of Investigation/LOI)
Query on LYA

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], J [auth C], L [auth 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 (Subject of Investigation/LOI)
Query on UMP

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], I [auth C], K [auth D]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LYA BindingDB:  1JUJ Ki: min: 1.3, max: 340 (nM) from 3 assay(s)
IC50: min: 70, max: 1.10e+5 (nM) from 9 assay(s)
PDBBind:  1JUJ Ki: 109 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.14α = 90
b = 98.14β = 110.7
c = 111.97γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations