6PBO

Staphylococcus aureus Dihydrofolate reductase in complex with NADPH and UCP1232


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.5 of the entry. See complete history


Literature

Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin ResistantStaphylococcus aureus.

Reeve, S.M.Si, D.Krucinska, J.Yan, Y.Viswanathan, K.Wang, S.Holt, G.T.Frenkel, M.S.Ojewole, A.A.Estrada, A.Agabiti, S.S.Alverson, J.B.Gibson, N.D.Priestley, N.D.Wiemer, A.J.Donald, B.R.Wright, D.L.

(2019) ACS Infect Dis 5: 1896-1906

  • DOI: https://doi.org/10.1021/acsinfecdis.9b00222
  • Primary Citation of Related Structures:  
    6P9Z, 6PBO

  • PubMed Abstract: 

    The spread of plasmid borne resistance enzymes in clinical Staphylococcus aureus isolates is rendering trimethoprim and iclaprim, both inhibitors of dihydrofolate reductase (DHFR), ineffective. Continued exploitation of these targets will require compounds that can broadly inhibit these resistance-conferring isoforms. Using a structure-based approach, we have developed a novel class of ionized nonclassical antifolates (INCAs) that capture the molecular interactions that have been exclusive to classical antifolates. These modifications allow for a greatly expanded spectrum of activity across these pathogenic DHFR isoforms, while maintaining the ability to penetrate the bacterial cell wall. Using biochemical, structural, and computational methods, we are able to optimize these inhibitors to the conserved active sites of the endogenous and trimethoprim resistant DHFR enzymes. Here, we report a series of INCA compounds that exhibit low nanomolar enzymatic activity and potent cellular activity with human selectivity against a panel of clinically relevant TMP resistant (TMP R ) and methicillin resistant Staphylococcus aureus (MRSA) isolates.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences , University of Connecticut , 69 N. Eagleville Road , Storrs , Connecticut 06269 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductaseA [auth X]157Staphylococcus aureusMutation(s): 0 
Gene Names: folA
EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus)
Explore P0A017 
Go to UniProtKB:  P0A017
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A017
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XNP
Query on XNP

Download Ideal Coordinates CCD File 
C [auth X]Tricyclic NADPH
C21 H30 N7 O17 P3
AJKICLDTLPZSPE-MTKBYBFRSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
D [auth X]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
O71 (Subject of Investigation/LOI)
Query on O71

Download Ideal Coordinates CCD File 
B [auth X](4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}phenyl)acetic acid
C25 H24 N4 O4
DFNOGZMANMBRCF-CQSZACIVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.94α = 90
b = 78.94β = 90
c = 108.27γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 A1104841

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2021-09-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2023-10-11
    Changes: Data collection, Refinement description