1TVE

Homoserine Dehydrogenase in complex with 4-(4-hydroxy-3-isopropylphenylthio)-2-isopropylphenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

New phenolic inhibitors of yeast homoserine dehydrogenase

Ejim, L.Mirza, I.A.Capone, C.Nazi, I.Jenkins, S.Chee, G.L.Berghuis, A.M.Wright, G.D.

(2004) Bioorg.Med.Chem. 12: 3825-3830

  • DOI: 10.1016/j.bmc.2004.05.009

  • PubMed Abstract: 
  • A relatively unexploited potential target for antimicrobial agents is the biosynthesis of essential amino acids. Homoserine dehydrogenase, which reduces aspartate semi-aldehyde to homoserine in a NAD(P)H-dependent reaction, is one such target that is ...

    A relatively unexploited potential target for antimicrobial agents is the biosynthesis of essential amino acids. Homoserine dehydrogenase, which reduces aspartate semi-aldehyde to homoserine in a NAD(P)H-dependent reaction, is one such target that is required for the biosynthesis of Met, Thr, and Ile from Asp. We report a small molecule screen of yeast homoserine dehydrogenase that has identified a new class of phenolic inhibitors of this class of enzyme. X-ray crystal structural analysis of one of the inhibitors in complex with homoserine dehydrogenase reveals that these molecules bind in the amino acid binding region of the active site and that the phenolic hydroxyl group interacts specifically with the backbone amide of Gly175. These results provide the first nonamino acid inhibitors of this class of enzyme and have the potential to be exploited as leads in antifungal compound design.


    Organizational Affiliation

    Antimicrobial Research Centre, Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, ON, Canada L8N 3Z5.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homoserine dehydrogenase
A, B
358Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HOM6
EC: 1.1.1.3
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
178
Query on 178

Download SDF File 
Download CCD File 
A, B
4-(4-HYDROXY-3-ISOPROPYLPHENYLTHIO)-2-ISOPROPYLPHENOL
C18 H22 O2 S
NEMLLZAROZVCCE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
178IC50: 2100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.289 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.456α = 90.00
b = 54.379β = 98.97
c = 92.497γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance