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

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.bmc.2004.05.009
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine dehydrogenase
A, B
358Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: hom6
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31116 
Go to UniProtKB:  P31116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31116
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 178

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C18 H22 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
178 PDBBind:  1TVE IC50: 2100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.289 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.456α = 90
b = 54.379β = 98.97
c = 92.497γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata 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: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description