3M08

Wild Type Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.014 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Inhibition of Antibiotic-Resistant Staphylococcus aureus by the Broad-Spectrum Dihydrofolate Reductase Inhibitor RAB1.

Bourne, C.R., Barrow, E.W., Bunce, R.A., Bourne, P.C., Berlin, K.D., Barrow, W.W.

(2010) Antimicrob.Agents Chemother. 54: 3825-3833

  • DOI: 10.1128/AAC.00361-10
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The bacterial burden on human health is quickly outweighing available therapeutics. Our long-term goal is the development of antimicrobials with the potential for broad-spectrum activity. We previously reported phthalazine-based inhibitors of dihydro ...

    The bacterial burden on human health is quickly outweighing available therapeutics. Our long-term goal is the development of antimicrobials with the potential for broad-spectrum activity. We previously reported phthalazine-based inhibitors of dihydrofolate reductase (DHFR) with potent activity against Bacillus anthracis, a major component of Project BioShield. The most active molecule, named RAB1, performs well in vitro and, in a cocrystal structure, was found deep within the active site of B. anthracis DHFR. We have now examined the activity of RAB1 against a panel of bacteria relevant to human health and found broad-spectrum applicability, particularly with regard to gram-positive organisms. RAB1 was most effective against Staphylococcus aureus, including methicillin- and vancomycin-resistant (MRSA/VRSA) strains. We have determined the cocrystal structure of the wild-type and trimethoprim-resistant (Phe 98 Tyr) DHFR enzyme from S. aureus with RAB1, and we found that rotational freedom of the acryloyl linker region allows the phthalazine moiety to occupy two conformations. This freedom in placement also allows either enantiomer of RAB1 to bind to S. aureus, in contrast to the specificity of B. anthracis for the S-enantiomer. Additionally, one of the conformations of RAB1 defines a unique surface cavity that increases the strength of interaction with S. aureus. These observations provide insights into the binding capacity of S. aureus DHFR and highlight atypical features critical for future exploitation in drug development.

    Related Citations: 
    • Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity
      Bourne, C.R.,Bunce, R.A.,Bourne, P.C.,Berlin, K.D.,Barrow, E.W.,Barrow, W.W.
      (2009) Antimicrob.agents chemother. 53: 3065

    Organizational Affiliation: 

    Department of Veterinary Pathobiology, 250 McElroy Hall, Oklahoma State University, Stillwater, OK 74078, USA. christina.bourne@okstate.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
161Staphylococcus aureusMutation(s): 0 
Gene Names: folA
EC: 1.5.1.3
Find proteins for P0A017 (Staphylococcus aureus)
Go to UniProtKB:  P0A017
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAR
Query on RAR
Download SDF File 
Download CCD File 
A
5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine
(S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-propylphthalazin-2(1H)-yl)prop-2-en-1-one
C27 H30 N6 O3
YGDVMSPWZQHNMB-NEQMZLFVSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP
Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RARKi: 0.9 nM (100) BINDINGDB
RARIC50: 2.9 - 12.5 nM (100) BINDINGDB
RARKi: 2.8 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.014 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.180α = 90.00
b = 79.180β = 90.00
c = 107.890γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance