3ARA

Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis and discovery of N-carbonylpyrrolidine- or N-sulfonylpyrrolidine-containing uracil derivatives as potent human deoxyuridine triphosphatase inhibitors

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

(2012) J.Med.Chem. 55: 2960-2969

  • DOI: 10.1021/jm201627n

  • PubMed Abstract: 
  • Recently, deoxyuridine triphosphatase (dUTPase) has emerged as a potential target for drug development as part of a new strategy of 5-fluorouracil-based combination chemotherapy. We have initiated a program to develop potent drug-like dUTPase inhibit ...

    Recently, deoxyuridine triphosphatase (dUTPase) has emerged as a potential target for drug development as part of a new strategy of 5-fluorouracil-based combination chemotherapy. We have initiated a program to develop potent drug-like dUTPase inhibitors based on structure-activity relationship (SAR) studies of uracil derivatives. N-Carbonylpyrrolidine- and N-sulfonylpyrrolidine-containing uracils were found to be promising scaffolds that led us to human dUTPase inhibitors (12k) having excellent potencies (IC(50) = 0.15 μM). The X-ray structure of a complex of 16a and human dUTPase revealed a unique binding mode wherein its uracil ring and phenyl ring occupy a uracil recognition region and a hydrophobic region, respectively, and are stacked on each other. Compounds 12a and 16a markedly enhanced the growth inhibition activity of 5-fluoro-2'-deoxyuridine against HeLa S3 cells in vitro (EC(50) = 0.27-0.30 μM), suggesting that our novel dUTPase inhibitors could contribute to the development of chemotherapeutic strategies when used in combination with TS inhibitors.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A, B, C
164Homo sapiensMutation(s): 0 
Gene Names: DUT
EC: 3.6.1.23
Find proteins for P33316 (Homo sapiens)
Go to Gene View: DUT
Go to UniProtKB:  P33316
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MKH
Query on MKH

Download SDF File 
Download CCD File 
A, B, C
1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione
C24 H27 N3 O5 S
NBGXNYZRJDHHHU-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MKHIC50: 320 - 480 nM (100) BINDINGDB
MKHIC50: 320 nM BINDINGMOAD
MKHIC50: 320 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.890α = 90.00
b = 83.263β = 90.00
c = 89.662γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CrystalCleardata reduction
CrystalCleardata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-30
    Type: Database references
  • Version 1.3: 2017-10-11
    Type: Refinement description