Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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)

Macromolecule Content

• Total Structure Weight: 62.56 kDa 
• Atom Count: 4649 
• Modelled Residue Count: 528 
• Deposited Residue Count: 528 
• Unique protein chains: 1

2KCE

BINDING OF THE ANTICANCER DRUG ZD1694 TO E. COLI THYMIDYLATE SYNTHASE: ASSESSING SPECIFICITY AND AFFINITY

• PDB DOI: 10.2210/pdb2KCE/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-06-09 Released: 1997-11-19 
• Deposition Author(s): Rutenber, E.E., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å

Literature

Binding of the anticancer drug ZD1694 to E. coli thymidylate synthase: assessing specificity and affinity.

Rutenber, E.E., Stroud, R.M.

(1996) Structure 4: 1317-1324

• PubMed: 8939755 
• DOI: 10.1016/s0969-2126(96)00139-6
• Primary Citation of Related Structures:  
  2KCE


• PubMed Abstract: 
  

Thymidylate synthase (TS) catalyzes the reductive methylation of deoxyuridine monophosphate (dUMP) by 5, 10-methylenetetrahydrofolate (CH2H4folate) to form deoxythymidine monophosphate (dTMP) and dihydrofolate (H2folate). The essential role of TS in the cell life cycle makes it an attractive target for the development of substrate and cofactor-based inhibitors that may find efficacy as anticancer and antiproliferative drugs. Antifolates that compete specifically with the binding of CH2H4 folate include the cofactor analog CB3717 (10-propargyl-5,8-dideazafolate). However, the development of potent cofactor analog inhibitors of TS, such as CB3717, as drugs has been slowed by their toxicity, which often becomes apparent as hepatic and renal toxicity mediated by the specific chemistry of the compound. Attempts to abolish toxicity in human patients while preserving potency against the target enzyme, have led to the development of ZD1694, which has already shown significant activity against colorectal tumours.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of California at San Francisco, 94143-0448, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B	264	Escherichia coli	Mutation(s): 0  Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D16	D [auth A], F [auth B]	TOMUDEX C21 H22 N4 O6 S IVTVGDXNLFLDRM-HNNXBMFYSA-N
UMP	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D16	PDBBind:  2KCE	Ki: 670 (nM) from 1 assay(s)
	Binding MOAD:  2KCE	Ki: 670 (nM) from 1 assay(s)
	BindingDB:  2KCE	IC50: 2300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.8	α = 90
b = 126.8	β = 90
c = 67.56	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SIEMENS	data reduction
SIEMENS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-06-09 
• Released Date: 1997-11-19 
Deposition Author(s): Rutenber, E.E., Stroud, R.M.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-10
  Changes: Non-polymer description