3DAT

Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of the ternary MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor design.

Bennett, B.C.Wan, Q.Ahmad, M.F.Langan, P.Dealwis, C.G.

(2009) J.Struct.Biol. 166: 162-171

  • Primary Citation of Related Structures:  3DAU

  • PubMed Abstract: 
  • For reasons of bioterrorism and drug resistance, it is imperative to identify and develop new molecular points of intervention against anthrax. Dihydrofolate reductase (DHFR) is a highly conserved enzyme and an established target in a number of speci ...

    For reasons of bioterrorism and drug resistance, it is imperative to identify and develop new molecular points of intervention against anthrax. Dihydrofolate reductase (DHFR) is a highly conserved enzyme and an established target in a number of species for a variety of chemotherapeutic programs. Recently, the crystal structure of Bacillus anthracis DHFR (baDHFR) in complex with methotrexate (MTX) was determined and, based on the structure, proposals were made for drug design strategies directed against the substrate-binding site. However, little is gleaned about the binding site for NADPH, the cofactor responsible for hydride transfer in the catalytic mechanism. In the present study, X-ray crystallography at 100 K was used to determine the structure of baDHFR in complex with MTX and NADPH. Although the NADPH binding mode is nearly identical to that seen in other DHFR ternary complex structures, the adenine moiety adopts an off-plane tilt of nearly 90 degrees and this orientation is stabilized by hydrogen bonds to functionally conserved Arg residues. A comparison of the binding site, focusing on this region, between baDHFR and the human enzyme is discussed, with an aim at designing species-selective therapeutics. Indeed, the ternary model, refined to 2.3 A resolution, provides an accurate template for testing the feasibility of identifying dual-site inhibitors, compounds that target both the substrate and cofactor-binding site. With the ternary model in hand, using in silico methods, several compounds were identified which could potentially form key bonding contacts in the substrate and cofactor-binding sites. Ultimately, two structurally distinct compounds were verified that inhibit baDHFR at low microM concentrations. The apparent Kd for one of these, (2-(3-(2-(hydroxyimino)-2-(pyridine-4-yl)-6,7-dimethylquinoxalin-2-yl)-1-(pyridine-4-yl)ethanone oxime), was measured by fluorescence spectroscopy to be 5.3 microM.


    Organizational Affiliation

    Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4965, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
162Bacillus 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
MTX
Query on MTX

Download SDF File 
Download CCD File 
A
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTXIC50: 12.2 - 24 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.900α = 90.00
b = 43.156β = 119.31
c = 67.870γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
REFMACphasing
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
BioCARSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2013-11-20
    Type: Non-polymer description
  • Version 1.3: 2017-10-25
    Type: Refinement description