3FY9

Staph. aureus DHFR F98Y complexed with AR-102


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


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Literature

Inhibitory properties and X-ray crystallographic study of the binding of AR-101, AR-102 and iclaprim in ternary complexes with NADPH and dihydrofolate reductase from Staphylococcus aureus

Oefner, C.Parisi, S.Schulz, H.Lociuro, S.Dale, G.E.

(2009) Acta Crystallogr D Biol Crystallogr 65: 751-757

  • DOI: 10.1107/S0907444909013936
  • Primary Citation of Related Structures:  
    3FY8, 3FY9, 3FYV, 3FYW

  • PubMed Abstract: 
  • Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S ...

    Iclaprim is a novel dihydrofolate reductase (DHFR) inhibitor belonging to the 2,4-diaminopyrimidine class of antibiotics, of which trimethoprim (TMP) is the most well known representative. Iclaprim exhibits potent bactericidal activity against major Gram-positive pathogens, notably methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) phenotypes, including TMP-resistant strains. The inhibition properties of racemic iclaprim and of the two enantiomers, termed AR-101 and AR-102, towards S. aureus wild-type DHFR and TMP-resistant F98Y mutant DHFR were determined and compared. Similar to TMP, AR-101, AR-102 and iclaprim are all competitive inhibitors with respect to the substrate dihydrofolate. Iclaprim, AR-101 and AR-102 demonstrated little or no difference in activity towards these enzymes and were significantly more potent than TMP. The crystal structures of S. aureus DHFR and F98Y mutant DHFR were determined as ternary complexes with NADPH and either AR-101, AR-102 or iclaprim. The binding modes of the inhibitors were analysed and compared. The X-ray crystallographic data explain the binding modes of all molecules well and can be used to rationalize the equipotent affinity of AR-101, AR-102 and iclaprim, which is also reflected in their antibacterial properties.


    Organizational Affiliation

    Arpida Ltd, CH-4153 Reinach, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrofolate reductaseA [auth X]158Staphylococcus aureusMutation(s): 1 
Gene Names: folA
EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus)
Explore P0A017 
Go to UniProtKB:  P0A017
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

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

Download Ideal Coordinates CCD File 
C [auth X]5-[[(2R)-2-cyclopropyl-7,8-dimethoxy-2H-chromen-5-yl]methyl]pyrimidine-2,4-diamine
C19 H22 N4 O3
HWJPWWYTGBZDEG-AWEZNQCLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
I2H BindingDB:  3FY9 Ki: min: 0.08, max: 0.08 (nM) from 2 assay(s)
IC50: min: 2.2, max: 7 (nM) from 3 assay(s)
XCF Binding MOAD:  3FY9 Ki: 3.5 (nM) from 1 assay(s)
BindingDB:  3FY9 IC50: 2.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.432α = 90
b = 79.432β = 90
c = 108.597γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-01-22 
  • Released Date: 2009-08-04 
  • Deposition Author(s): Oefner, C.

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance