4DB7

Crystal structure of B. anthracis DHPS with compound 25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity.

Zhao, Y.Hammoudeh, D.Yun, M.K.Qi, J.White, S.W.Lee, R.E.

(2012) Chemmedchem 7: 861-870

  • DOI: 10.1002/cmdc.201200049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is ...

    Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is highly conserved and is distinct from the sulfonamide binding site. It therefore represents an attractive alternative target for the design of novel antibacterial agents. We previously carried out the structural characterization of a known pyridazine inhibitor in the Bacillus anthracis DHPS pterin site and identified a number of unfavorable interactions that appear to compromise binding. With this structural information, a series of 4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazines were designed to improve binding affinity. Most importantly, the N-methyl ring substitution was removed to improve binding within the pterin pocket, and the length of the side chain carboxylic acid was optimized to fully engage the pyrophosphate binding site. These inhibitors were synthesized and evaluated by an enzyme activity assay, X-ray crystallography, isothermal calorimetry, and surface plasmon resonance to obtain a comprehensive understanding of the binding interactions from structural, kinetic, and thermodynamic perspectives. This study clearly demonstrates that compounds lacking the N-methyl substitution exhibit increased inhibition of DHPS, but the beneficial effects of optimizing the side chain length are less apparent.


    Organizational Affiliation

    Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydropteroate Synthase
A, B
297Bacillus anthracisMutation(s): 0 
Gene Names: folP
EC: 2.5.1.15
Find proteins for Q81VW8 (Bacillus anthracis)
Go to UniProtKB:  Q81VW8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Z25
Query on Z25

Download SDF File 
Download CCD File 
A, B
3-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)propanoic acid
C9 H9 N5 O4
CGUTUVAIFLDCOT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z25IC50: 36000 nM BINDINGMOAD
Z25Kd: 273 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.232 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.695α = 90.00
b = 99.695β = 90.00
c = 263.431γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SERGUIdata collection
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2012-05-09
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description