Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.24 kDa 
• Atom Count: 1497 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

3FRF

S. aureus DHFR complexed with NADPH and iclaprim

• PDB DOI: 10.2210/pdb3FRF/pdb

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


• Deposited: 2009-01-08 Released: 2010-01-12 
• Deposition Author(s): Oefner, C., Dale-Glenn, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Increased hydrophobic interactions of iclaprim with Staphylococcus aureus dihydrofolate reductase are responsible for the increase in affinity and antibacterial activity

Oefner, C., Bandera, M., Haldimann, A., Laue, H., Schulz, H., Mukhija, S., Parisi, S., Weiss, L., Lociuro, S., Dale, G.E.

(2009) J Antimicrob Chemother 63: 687-698

• PubMed: 19211577 
• DOI: 10.1093/jac/dkp024
• Primary Citation of Related Structures:  
  3FRA, 3FRB, 3FRD, 3FRE, 3FRF


• PubMed Abstract: 
  

Iclaprim is a novel 2,4-diaminopyrimidine that exhibits potent, rapid bactericidal activity against major Gram-positive pathogens, including methicillin-susceptible Staphylococcus aureus and methicillin-resistant S. aureus, and is currently in clinical development for the treatment of complicated skin and skin structure infections. An understanding of the known mechanism of resistance to trimethoprim led to the design of this new inhibitor, with improved affinity towards dihydrofolate reductase (DHFR) from S. aureus and clinically useful activity against S. aureus including isolates resistant to trimethoprim. The objective of this study was to characterize the mode of action of iclaprim and its inhibitory properties against DHFR.

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Organizational Affiliation: 

Arpida AG, Duggingerstrasse 23, CH-4153 Reinach, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	158	Staphylococcus aureus	Mutation(s): 0  Gene Names: folA EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus) Explore P0A017  Go to UniProtKB:  P0A017

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth X]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
XCF	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

Binding Affinity Annotations
ID	Source	Binding Affinity
XCF	Binding MOAD:  3FRF	Ki: 3 (nM) from 1 assay(s)
	BindingDB:  3FRF	IC50: 2.9 (nM) from 1 assay(s)
I2H	BindingDB:  3FRF	Ki: min: 0.08, max: 0.08 (nM) from 2 assay(s)
		IC50: min: 2.2, max: 7 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.287 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.279	α = 90
b = 79.279	β = 90
c = 108.165	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-08 
• Released Date: 2010-01-12 
Deposition Author(s): Oefner, C., Dale-Glenn, E.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-20
  Changes: Non-polymer description