Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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 | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 135.83 kDa 
• Atom Count: 10136 
• Modelled Residue Count: 1152 
• Deposited Residue Count: 1152 
• Unique protein chains: 1

1HVY

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

• PDB DOI: 10.2210/pdb1HVY/pdb

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


• Deposited: 2001-01-08 Released: 2001-01-31 
• Deposition Author(s): Phan, J., Koli, S., Minor, W., Dunlap, R.B., Berger, S.H., Lebioda, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

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: 11329255 
• DOI: 10.1021/bi002413i
• Primary Citation of Related Structures:  
  1HVY


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B, C, D	288	Homo sapiens	Mutation(s): 1  Gene Names: TYMS, TS, OK/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 GTEx:  ENSG00000176890

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D16	E [auth A], H [auth B], K [auth C], N [auth D]	TOMUDEX C21 H22 N4 O6 S IVTVGDXNLFLDRM-HNNXBMFYSA-N
UMP	F [auth A], I [auth B], L [auth C], O [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
BME	G [auth A], J [auth B], M [auth C], P [auth D]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
D16	PDBBind:  1HVY	IC50: 290 (nM) from 1 assay(s)
	BindingDB:  1HVY	IC50: 2.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.849	α = 70.23
b = 70.495	β = 83.29
c = 74.533	γ = 73.28

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-08 
• Released Date: 2001-01-31 
Deposition Author(s): Phan, J., Koli, S., Minor, W., Dunlap, R.B., Berger, S.H., Lebioda, L.

Revision History  

• Version 1.0: 2001-01-31
  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: 2012-10-10
  Changes: Non-polymer description
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary