3EEM

Candida glabrata Dihydrofolate Reductase complexed with 2,4-diamino-5-[3-methyl-3-(3-methoxy-5-(2,6-dimethylphenyl)phenyl)prop-1-ynyl]-6-methylpyrimidine(UCP111D26M) and NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Probing the active site of Candida glabrata dihydrofolate reductase with high resolution crystal structures and the synthesis of new inhibitors

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

(2009) Chem Biol Drug Des 73: 62-74

  • DOI: 10.1111/j.1747-0285.2008.00745.x
  • Primary Citation of Related Structures:  
    3EEK, 3EEL, 3EEM, 3EEJ

  • PubMed Abstract: 
  • Candida glabrata, a fungal strain resistant to many commonly administered antifungal agents, has become an emerging threat to human health. In previous work, we validated that the essential enzyme, dihydrofolate reductase, is a drug target in C. glab ...

    Candida glabrata, a fungal strain resistant to many commonly administered antifungal agents, has become an emerging threat to human health. In previous work, we validated that the essential enzyme, dihydrofolate reductase, is a drug target in C. glabrata. Using a crystal structure of dihydrofolate reductase from C. glabrata bound to an initial lead compound, we designed a class of biphenyl antifolates that potently and selectively inhibit both the enzyme and the growth of the fungal culture. In this work, we explore the structure-activity relationships of this class of antifolates with four new high resolution crystal structures of enzyme:inhibitor complexes and the synthesis of four new inhibitors. The designed inhibitors are intended to probe key hydrophobic pockets visible in the crystal structure. The crystal structures and an evaluation of the new compounds reveal that methyl groups at the meta and para positions of the distal phenyl ring achieve the greatest number of interactions with the pathogenic enzyme and the greatest degree of selectivity over the human enzyme. Additionally, antifungal activity can be tuned with substitution patterns at the propargyl and para-phenyl positions.


    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrofolate reductaseAB227[Candida] glabrataMutation(s): 0 
Gene Names: CAGL0J03894g
EC: 1.5.1.3
Find proteins for Q6FPH0 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Explore Q6FPH0 
Go to UniProtKB:  Q6FPH0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
53V
Query on 53V

Download CCD File 
A, B
5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
C24 H26 N4 O
XZXVRKHUCSXVBM-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
52VIC50:  5.5   nM  BindingDB
53VIC50:  5.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.822α = 90
b = 42.822β = 90
c = 231.532γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-09-04 
  • Released Date: 2009-08-18 
  • Deposition Author(s): Liu, J., Anderson, A.

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Non-polymer description
  • Version 1.3: 2017-10-25
    Changes: Refinement description