3FL8

Crystal structure of B. anthracis dihydrofolate reductase (DHFR) with RAB1, a TMP-dihydrophthalazine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2881 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 3065-3073

  • DOI: 10.1128/AAC.01666-08
  • Primary Citation of Related Structures:  3FL9

  • PubMed Abstract: 
  • Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously repo ...

    Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (< or =12.8 microg/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2(1)2(1)2(1), and X-ray diffraction data were collected to a 2.3-A resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.


    Organizational Affiliation

    Department of Veterinary Pathobiology, 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, B, C, D, E, F, G, H
166Bacillus anthracisGene Names: dfrA (dfrD)
EC: 1.5.1.3
Find proteins for Q81R22 (Bacillus anthracis)
Go to UniProtKB:  Q81R22
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAR
Query on RAR

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
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
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RARIC50: 54 nM (100) BINDINGDB
RARIC50: 54 nM BINDINGMOAD
RARIC50: 54 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2881 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.178α = 90.00
b = 135.920β = 90.00
c = 168.652γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
PHENIXrefinement
SADABSdata scaling
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance