4ISK

Crystal structure of E.coli thymidylate synthase with dUMP and the BGC 945 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development and Binding Mode Assessment of N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-gamma-glutamyl-d-glutamic Acid (BGC 945), a Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells.

Tochowicz, A.Dalziel, S.Eidam, O.O'Connell, J.D.Griner, S.Finer-Moore, J.S.Stroud, R.M.

(2013) J Med Chem 56: 5446-5455

  • DOI: https://doi.org/10.1021/jm400490e
  • Primary Citation of Related Structures:  
    4ISK

  • PubMed Abstract: 

    N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-γ-glutamyl-d-glutamic acid 1 (BGC 945, now known as ONX 0801), is a small molecule thymidylate synthase (TS) inhibitor discovered at the Institute of Cancer Research in London. It is licensed by Onyx Pharmaceuticals and is in phase 1 clinical studies. It is a novel antifolate drug resembling TS inhibitors plevitrexed and raltitrexed that combines enzymatic inhibition of thymidylate synthase with α-folate receptor-mediated targeting of tumor cells. Thus, it has potential for efficacy with lower toxicity due to selective intracellular accumulation through α-folate receptor (α-FR) transport. The α-FR, a cell-surface receptor glycoprotein, which is overexpressed mainly in ovarian and lung cancer tumors, has an affinity for 1 similar to that for its natural ligand, folic acid. This study describes a novel synthesis of 1, an X-ray crystal structure of its complex with Escherichia coli TS and 2'-deoxyuridine-5'-monophosphate, and a model for a similar complex with human TS.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California-San Francisco , 600 16th Street, San Francisco, California 94158, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
264Escherichia coli K-12Mutation(s): 0 
Gene Names: thyAb2827JW2795
EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A884
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1JY
Query on 1JY

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
K [auth A]
N [auth B]
Q [auth C]
BA [auth G],
EA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Y [auth F]
N-(4-{[(6S)-2-(hydroxymethyl)-4-oxo-4,6,7,8-tetrahydro-1H-cyclopenta[g]quinazolin-6-yl](prop-2-yn-1-yl)amino}benzoyl)-L-gamma-glutamyl-D-glutamic acid
C32 H33 N5 O10
NVHRBQOZEMFKLD-CUYJMHBOSA-N
UMC
Query on UMC

Download Ideal Coordinates CCD File 
CA [auth H],
L [auth B],
R [auth D],
U [auth E],
X [auth F]
2'-deoxy-5'-uridylic acid
C9 H15 N2 O8 P
WQQZADPPRABIFU-SHYZEUOFSA-N
UMP
Query on UMP

Download Ideal Coordinates CCD File 
I [auth A],
O [auth C],
Z [auth G]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
J [auth A]
M [auth B]
P [auth C]
AA [auth G],
DA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.9α = 90
b = 85.5β = 109.4
c = 134.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary