Candida glabrata Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structure-guided development of efficacious antifungal agents targeting Candida glabrata dihydrofolate reductase.

Liu, J.Bolstad, D.B.Smith, A.E.Priestley, N.D.Wright, D.L.Anderson, A.C.

(2008) Chem Biol 15: 990-996

  • DOI: https://doi.org/10.1016/j.chembiol.2008.07.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Candida glabrata is a lethal fungal pathogen resistant to many antifungal agents and has emerged as a critical target for drug discovery. Over the past several years, we have been developing a class of propargyl-linked antifolates as antimicrobials and hypothesized that these compounds could be effective inhibitors of dihydrofolate reductase (DHFR) from C. glabrata. We initially screened a small collection of these inhibitors and found modest levels of potency. Subsequently, we determined the crystal structure of C. glabrata DHFR bound to a representative inhibitor with data to 1.6 A resolution. Using this structure, we designed and synthesized second-generation inhibitors. These inhibitors bind the C. glabrata DHFR enzyme with subnanomolar potency, display greater than 2000-fold levels of selectivity over the human enzyme, and inhibit the growth of C. glabrata at levels observed with clinically employed therapeutics.

  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Road, Storrs, CT 0626, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase
A, B
227Nakaseomyces glabratusMutation(s): 0 
Gene Names: DHFR
Find proteins for Q6FPH0 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138))
Explore Q6FPH0 
Go to UniProtKB:  Q6FPH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FPH0
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
N22 Binding MOAD:  3CSE IC50: 8.2 (nM) from 1 assay(s)
BindingDB:  3CSE IC50: 8.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.69α = 90
b = 42.69β = 90
c = 230.404γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-27
    Changes: Non-polymer description
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations