3FL9

Crystal structure of B. anthracis dihydrofolate reductase (DHFR) with trimethoprim


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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This is version 1.2 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:  
    3FL8, 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 reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dihydrofolate reductase (DHFR)
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
166Bacillus anthracisMutation(s): 0 
Gene Names: BAS2083BA_2237dfrADHFRGBAA2237GBAA_2237
EC: 1.5.1.3
UniProt
Find proteins for Q81R22 (Bacillus anthracis)
Explore Q81R22 
Go to UniProtKB:  Q81R22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81R22
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOP
Query on TOP

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
TRIMETHOPRIM
C14 H18 N4 O3
IEDVJHCEMCRBQM-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TOP BindingDB:  3FL9 Ki: 2.41e+4 (nM) from 1 assay(s)
IC50: min: 4.30e+4, max: 7.73e+4 (nM) from 5 assay(s)
Binding MOAD:  3FL9 IC50: 7.72e+7 (nM) from 1 assay(s)
PDBBind:  3FL9 IC50: 7.72e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.93α = 90
b = 67.61β = 90.12
c = 167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model