3H26

Structural Studies of Pterin-Based Inhibitors of Dihydropteroate Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies of pterin-based inhibitors of dihydropteroate synthase.

Hevener, K.E.Yun, M.K.Qi, J.Kerr, I.D.Babaoglu, K.Hurdle, J.G.Balakrishna, K.White, S.W.Lee, R.E.

(2010) J.Med.Chem. 53: 166-177

  • DOI: 10.1021/jm900861d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the target of the sulfonamide class of antibacterials. Resistance and toxicities associated with sulfonamides have led to a decrease in their clinical use. Compounds th ...

    Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the target of the sulfonamide class of antibacterials. Resistance and toxicities associated with sulfonamides have led to a decrease in their clinical use. Compounds that bind to the pterin binding site of DHPS, as opposed to the p-amino benzoic acid (pABA) binding site targeted by the sulfonamide agents, are anticipated to bypass sulfonamide resistance. To identify such inhibitors and map the pterin binding pocket, we have performed virtual screening, synthetic, and structural studies using Bacillus anthracis DHPS. Several compounds with inhibitory activity have been identified, and crystal structures have been determined that show how the compounds engage the pterin site. The structural studies identify the key binding elements and have been used to generate a structure-activity based pharmacophore map that will facilitate the development of the next generation of DHPS inhibitors which specifically target the pterin site.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Avenue, Room 327 Johnson Building, Memphis, Tennessee 38163, 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
B56
Query on B56

Download SDF File 
Download CCD File 
A, B
2-amino-8-methyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxylic acid
C8 H9 N5 O3
LLLLJZKILITAII-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B56IC50: 32400 nM (99) BINDINGDB
B56Kd: 5260 nM (99) BINDINGDB
B56IC50: 32400 nM BINDINGMOAD
B56IC50: 32400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.899α = 90.00
b = 97.899β = 90.00
c = 262.880γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description