5U12

E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase.

Dennis, M.L.Lee, M.D.Harjani, J.R.Ahmed, M.DeBono, A.J.Pitcher, N.P.Wang, Z.C.Chhabra, S.Barlow, N.Rahmani, R.Cleary, B.Dolezal, O.Hattarki, M.Aurelio, L.Shonberg, J.Graham, B.Peat, T.S.Baell, J.B.Swarbrick, J.D.

(2018) Chemistry 24: 1922-1930

  • DOI: 10.1002/chem.201704730
  • Primary Citation of Related Structures:  
    5U10, 5U0Y, 5U0Z, 5U12, 5U11, 5U14, 5U13, 5U0W, 5U0V, 5V7A

  • PubMed Abstract: 
  • Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA ...

    Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA. In the wake of sulfa drug resistance, targeting the structurally rigid (and more conserved) pterin site has been proposed as an alternate strategy to inhibit DHPS in wild-type and sulfa drug resistant strains. Following the work on developing pterin-site inhibitors of the adjacent enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), we now present derivatives of 8-mercaptoguanine, a fragment that binds weakly within both enzymes, and quantify sub-μm binding using surface plasmon resonance (SPR) to Escherichia coli DHPS (EcDHPS). Eleven ligand-bound EcDHPS crystal structures delineate the structure-activity relationship observed providing a structural framework for the rational development of novel, substrate-envelope-compliant DHPS inhibitors.


    Organizational Affiliation

    Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydropteroate synthase AB284Escherichia coli CFT073Mutation(s): 0 
Gene Names: folPc3933
EC: 2.5.1.15
Find proteins for P0AC14 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P0AC14 
Go to UniProtKB:  P0AC14
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5RU
Query on 5RU

Download Ideal Coordinates CCD File 
A, B
2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one
C12 H10 F N5 O S
DBXBVKPIQPXRBY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.887α = 90
b = 84.546β = 109.87
c = 84.145γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references