4H96

Candida albicans dihydrofolate reductase complexed with NADPH and 5-{3-[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-methoxyphenyl]prop-1-yn-1-yl}-6-ethylpyrimidine-2,4-diamine (UCP1018)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of the active sites of dihydrofolate reductase from two species of Candida uncovers ligand-induced conformational changes shared among species.

Paulsen, J.L.Viswanathan, K.Wright, D.L.Anderson, A.C.

(2013) Bioorg Med Chem Lett 23: 1279-1284

  • DOI: https://doi.org/10.1016/j.bmcl.2013.01.008
  • Primary Citation of Related Structures:  
    3RO9, 3ROA, 4H95, 4H96, 4H97, 4H98

  • PubMed Abstract: 

    A novel strategy for targeting the pathogenic organisms Candida albicans and Candida glabrata focuses on the development of potent and selective antifolates effective against dihydrofolate reductase. Crystal structure analysis suggested that an essential loop at the active site (Thr 58-Phe 66) differs from the analogous residues in the human enzyme, potentially providing a mechanism for achieving selectivity. In order to probe the role of this loop, we employed chemical synthesis, crystal structure determination and molecular dynamics simulations. The results of these analyses show that the loop residues undergo ligand-induced conformational changes that are similar among the fungal and human species.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate Reductase
A, B
189Candida albicansMutation(s): 0 
Gene Names: DFR1DHFR
EC: 1.5.1.3
UniProt
Find proteins for P22906 (Candida albicans)
Explore P22906 
Go to UniProtKB:  P22906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22906
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
14Q
Query on 14Q

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
5-{3-[3-(1,3-benzodioxol-5-yl)-5-methoxyphenyl]prop-1-yn-1-yl}-6-ethylpyrimidine-2,4-diamine
C23 H22 N4 O3
DEWBMLVREOXAJX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.665α = 90
b = 118.665β = 90
c = 39.331γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Non-polymer description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description