4ISK | pdb_00004isk

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 252.3 kDa 
  • Atom Count: 18,782 
  • Modeled Residue Count: 2,112 
  • Deposited Residue Count: 2,112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
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

View Full Validation Report



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