5JQ9

Yersinia pestis DHPS with pterine-sulfa conjugate Compound 16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Pterin-sulfa conjugates as dihydropteroate synthase inhibitors and antibacterial agents.

Zhao, Y.Shadrick, W.R.Wallace, M.J.Wu, Y.Griffith, E.C.Qi, J.Yun, M.K.White, S.W.Lee, R.E.

(2016) Bioorg.Med.Chem.Lett. 26: 3950-3954

  • DOI: 10.1016/j.bmcl.2016.07.006

  • PubMed Abstract: 
  • The sulfonamide class of antibiotics has been in continuous use for over 70years. They are thought to act by directly inhibiting dihydropteroate synthase (DHPS), and also acting as prodrugs that sequester pterin pools by forming dead end pterin-sulfo ...

    The sulfonamide class of antibiotics has been in continuous use for over 70years. They are thought to act by directly inhibiting dihydropteroate synthase (DHPS), and also acting as prodrugs that sequester pterin pools by forming dead end pterin-sulfonamide conjugates. In this study, eight pterin-sulfonamide conjugates were synthesized using a novel synthetic strategy and their biochemical and microbiological properties were investigated. The conjugates were shown to competitively inhibit DHPS, and inhibition was enhanced by the presence of pyrophosphate that is crucial to catalysis and is known to promote an ordering of the DHPS active site. The co-crystal structure of Yersinia pestis DHPS bound to one of the more potent conjugates revealed a mode of binding that is similar to that of the enzymatic product analog pteroic acid. The antimicrobial activities of the pterin-sulfonamide conjugates were measured against Escherichia coli in the presence and absence of folate precursors and dependent metabolites. These results show that the conjugates have appreciable antibacterial activity and act by an on target, anti-folate pathway mechanism rather than as simple dead end products.


    Organizational Affiliation

    Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 1000, Memphis, TN 38105, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydropteroate synthase
A, B
279Yersinia pestisMutation(s): 0 
Gene Names: dhpS
EC: 2.5.1.15
Find proteins for Q7CKJ1 (Yersinia pestis)
Go to UniProtKB:  Q7CKJ1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6MB
Query on 6MB

Download SDF File 
Download CCD File 
A, B
4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide
C18 H18 N8 O4 S
JJZFSJXETRBCPR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.687α = 90.00
b = 49.897β = 89.78
c = 74.279γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-04 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Wu, Y., White, S.W.

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations