4FS3

Crystal structure of Staphylococcus aureus enoyl-ACP reductase in complex with NADP and AFN-1252


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mode of Action, In Vitro Activity, and In Vivo Efficacy of AFN-1252, a Selective Antistaphylococcal FabI Inhibitor.

Kaplan, N.Albert, M.Awrey, D.Bardouniotis, E.Berman, J.Clarke, T.Dorsey, M.Hafkin, B.Ramnauth, J.Romanov, V.Schmid, M.B.Thalakada, R.Yethon, J.Pauls, H.W.

(2012) Antimicrob Agents Chemother 56: 5865-5874

  • DOI: https://doi.org/10.1128/AAC.01411-12
  • Primary Citation of Related Structures:  
    4FS3

  • PubMed Abstract: 

    The mechanism of action of AFN-1252, a selective inhibitor of Staphylococcus aureus enoyl-acyl carrier protein reductase (FabI), which is involved in fatty acid biosynthesis, was confirmed by using biochemistry, macromolecular synthesis, genetics, and cocrystallization of an AFN-1252-FabI complex. AFN-1252 demonstrated a low propensity for spontaneous resistance development and a time-dependent reduction of the viability of both methicillin-susceptible and methicillin-resistant S. aureus, achieving a ≥2-log(10) reduction in S. aureus counts over 24 h, and was extremely potent against clinical isolates of S. aureus (MIC(90), 0.015 μg/ml) and coagulase-negative staphylococci (MIC(90), 0.12 μg/ml), regardless of their drug resistance, hospital- or community-associated origin, or other clinical subgroup. AFN-1252 was orally available in mouse pharmacokinetic studies, and a single oral dose of 1 mg/kg AFN-1252 was efficacious in a mouse model of septicemia, providing 100% protection from an otherwise lethal peritoneal infection of S. aureus Smith. A median effective dose of 0.15 mg/kg indicated that AFN-1252 was 12 to 24 times more potent than linezolid in the model. These studies, demonstrating a selective mode of action, potent in vitro activity, and in vivo efficacy, support the continued investigation of AFN-1252 as a targeted therapeutic for staphylococcal infections.


  • Organizational Affiliation

    Affinium Pharmaceuticals, Inc., Toronto, ON, Canada. nkaplan@afnm.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI256Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: fabISAR0978
EC: 1.3.1.10
UniProt
Find proteins for Q6GI75 (Staphylococcus aureus (strain MRSA252))
Explore Q6GI75 
Go to UniProtKB:  Q6GI75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GI75
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0WD
Query on 0WD

Download Ideal Coordinates CCD File 
B [auth A][[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate
C21 H30 N7 O17 P3
ONOVTRNLNDQWGA-NNYOXOHSSA-N
0WE
Query on 0WE

Download Ideal Coordinates CCD File 
C [auth A]N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide
C22 H23 N3 O3
WDNCPCMRTFYNIQ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0WE Binding MOAD:  4FS3 Ki: 12.8 (nM) from 1 assay(s)
PDBBind:  4FS3 IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.269α = 90
b = 126.269β = 90
c = 80.913γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description