Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 145976.78 
• Atom Count: 9445 
• Residue Count: 1252 
• Unique protein chains: 1

1JU6

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

• DOI: 10.2210/pdb1JU6/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2001-08-23 Released: 2001-09-19 
• Deposition Author(s): Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M.

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Experimental Data Snapshot

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

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

• PubMed: 11697906 
• DOI: 10.1006/jmbi.2001.5074
• Primary Citation of Related Structures:  
  1JUT, 1JUJ, 1JTU, 1JTQ


• 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 2.2-3.0 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
THYMIDYLATE SYNTHASE	A, B, C, D	313	Homo sapiens	Mutation(s): 1  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
LYA	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 LY231514 C20 H21 N5 O6 WBXPDJSOTKVWSJ-ZDUSSCGKSA-N
UMP	A, B, C, D	2'-DEOXYURIDINE 5'-MONOPHOSPHATE DUMP C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LYA	IC50: 5700 - 110000 nM (99) BINDINGDB
LYA	Ki: 1.3 - 340 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.264 
• R-Value Work: 0.236 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 68.138	α = 71.67
b = 69.633	β = 85.72
c = 73.958	γ = 75.11

Software Package:

Software Name	Purpose
CNS	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-23 
• Released Date: 2001-09-19 
• Deposition Author(s): Sayre, P.H., Finer-Moore, J.S., Fritz, T.A., Biermann, D., Gates, S.B., MacKellar, W.C., Patel, V.F., Stroud, R.M.

Revision History 

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