9DAR | pdb_00009dar

Structure of E. coli dihydrofolate reductase (DHFR) in an occluded conformation and in complex with cycloguanil

  • Classification: OXIDOREDUCTASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-08-22 Released: 2025-02-26 
  • Deposition Author(s): Berkovich, D.A., Jez, J.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9DAR

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Expanding the Landscape of Dual Action Antifolate Antibacterials through 2,4-Diamino-1,6-dihydro-1,3,5-triazines.

Georgiades, J.D.Berkovich, D.A.McKee, S.R.Smith, A.R.Sankaran, B.Flentie, K.N.Castaneda, C.H.Grohmann, D.G.Rohatgi, R.Lasky, C.Mason, T.A.Champine, J.E.Miller, P.A.Mollmann, U.Moraski, G.C.Franzblau, S.G.Miller, M.J.Stallings, C.L.Jez, J.M.Hathaway, B.A.Wencewicz, T.A.

(2025) ACS Infect Dis 11: 689-702

  • DOI: https://doi.org/10.1021/acsinfecdis.4c00768
  • Primary Citation Related Structures: 
    9DAQ, 9DAR

  • PubMed Abstract: 

    Antibiotics that operate via multiple mechanisms of action are a promising strategy to combat growing resistance. Previous studies have shown that dual action antifolates formed from a pyrroloquinazolinediamine core can inhibit the growth of bacterial pathogens without developing resistance. In this work, we expand the scope of dual action antifolates by repurposing the 2,4-diamino-1,6-dihydro-1,3,5-triazine (DADHT) cycloguanil scaffold to a variety of derivatives designed to inhibit dihydrofolate reductase (DHFR) and disrupt bacterial membranes. Dual mechanism DADHTs have activity against a variety of target pathogens, including Mycobacterium tuberculosis , Mycobacterium abscessus , and Pseudomonas aeruginosa , among other ESKAPEE organisms. Through X-ray crystallography, we confirmed engagement of the Escherichia coli DHFR target and found that some DADHTs stabilize a previously unobserved conformation of the enzyme but, broadly, bind in the occluded conformation. Using in vitro inhibition of purified E. coli and Staphylococcus aureus DHFR and disruption of E. coli membranes, we determined that alkyl substitution of dihydrotriazine at the 6-position best optimizes the DADHT's two mechanisms of action. By employing both mechanisms, the DADHT spectrum of activity was extended beyond the scope of traditional antifolates. We are optimistic that the dual mechanism approach, particularly through the action of antifolates, offers a unique means of combating hard-to-treat bacterial infections.


  • Organizational Affiliation
    • Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States.

Macromolecule Content 

  • Total Structure Weight: 18.69 kDa 
  • Atom Count: 1,372 
  • Modeled Residue Count: 161 
  • Deposited Residue Count: 161 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrofolate reductase161Escherichia coliMutation(s): 0 
Gene Names: folAc0058
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABQ4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1CY
(Subject of Investigation/LOI)

Query on 1CY



Download:Ideal Coordinates CCD File
B [auth A]1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine
C11 H14 Cl N5
QMNFFXRFOJIOKZ-UHFFFAOYSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
C [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.076α = 90
b = 68.076β = 90
c = 212.602γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1P30GM124169
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI171514
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2U01AI123394

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references