3ARN

Human dUTPase in complex with novel uracil derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of a novel class of potent human deoxyuridine triphosphatase inhibitors remarkably enhancing the antitumor activity of thymidylate synthase inhibitors

Miyahara, S.Miyakoshi, H.Yokogawa, T.Chong, K.T.Taguchi, J.Muto, T.Endoh, K.Yano, W.Wakasa, T.Ueno, H.Takao, Y.Fujioka, A.Hashimoto, A.Itou, K.Yamamura, K.Nomura, M.Nagasawa, H.Shuto, S.Fukuoka, M.

(2012) J Med Chem 55: 2970-2980

  • DOI: 10.1021/jm201628y
  • Primary Citation of Related Structures:  
    3ARN

  • PubMed Abstract: 
  • Inhibition of human deoxyuridine triphosphatase (dUTPase) has been identified as a promising approach to enhance the efficacy of 5-fluorouracil (5-FU)-based chemotherapy. This study describes the development of a novel class of dUTPase inhibitors bas ...

    Inhibition of human deoxyuridine triphosphatase (dUTPase) has been identified as a promising approach to enhance the efficacy of 5-fluorouracil (5-FU)-based chemotherapy. This study describes the development of a novel class of dUTPase inhibitors based on the structure-activity relationship (SAR) studies of uracil derivatives. Starting from the weak inhibitor 7 (IC(50) = 100 μM), we developed compound 26, which is the most potent human dUTPase inhibitor (IC(50) = 0.021 μM) reported to date. Not only does compound 26 significantly enhance the growth inhibition activity of 5-fluoro-2'-deoxyuridine (FdUrd) against HeLa S3 cells in vitro (EC(50) = 0.075 μM) but also shows robust antitumor activity against MX-1 breast cancer xenograft model in mice when administered orally with a continuous infusion of 5-FU. This is the first in vivo evidence that human dUTPase inhibitors enhance the antitumor activity of TS inhibitors. On the basis of these findings, it was concluded that compound 26 is a promising candidate for clinical development.


    Related Citations: 
    • Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors
      Miyakoshi, H., Miyahara, S., Chong, K.T., Fukuoka, M.
      () To be published --: --

    Organizational Affiliation

    Tsukuba Research Center, Taiho Pharmaceutical Co. Ltd., Okubo 3, Tsukuba, Ibaraki 300-2611, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolaseABC164Homo sapiensMutation(s): 0 
Gene Names: DUT
EC: 3.6.1.23
Find proteins for P33316 (Homo sapiens)
Explore P33316 
Go to UniProtKB:  P33316
NIH Common Fund Data Resources
PHAROS  P33316
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSJ
Query on MSJ

Download CCD File 
A, B, C
N-{5-[(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)methoxy]-2-methylpentan-2-yl}benzenesulfonamide
C17 H23 N3 O5 S
RMYLCQFHDYJCJN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MSJIC50:  3900   nM  Binding MOAD
MSJIC50:  9480   nM  BindingDB
MSJIC50 :  3900   nM  PDBBind
MSJIC50:  3900   nM  BindingDB
MSJEC50:  5100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.404α = 90
b = 83.147β = 90
c = 89.586γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-30
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description