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.

doi:10.2210/pdb3frf/pdb

Macromolecule Content

Total Structure Weight: 19244.56
Atom Count: 1355
Residue Count: 158
Unique protein chains: 1

3FRF

S. aureus DHFR complexed with NADPH and iclaprim

DOI: 10.2210/pdb3FRF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.287
R-Value Work: 0.228

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1093/jac/dkp024
Primary Citation of Related Structures:
3FRE, 3FRD, 3FRB, 3FRA

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrofolate reductase	X	158	Staphylococcus aureus	Mutation(s): 0 Gene Names: folA EC: 1.5.1.3
Find proteins for P0A017 (Staphylococcus aureus) Go to UniProtKB: P0A017
Protein Feature View Full Protein Feature View for P0A017

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
XCF Query on XCF Download SDF File Download CCD File	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
NDP Query on NDP Download SDF File Download CCD File	X	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
XCF	IC50: 2.9 nM (100) BINDINGDB
I2H	IC50: 2.2 - 7 nM (100) BINDINGDB
I2H	Ki: 0.1 nM (100) BINDINGDB
XCF	Ki: 3 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.287
R-Value Work: 0.228
Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.279	α = 90.00
b = 79.279	β = 90.00
c = 108.165	γ = 120.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

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
Type: Version format compliance
Version 1.2: 2013-11-20
Type: Non-polymer description

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

148037 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3FRF

S. aureus DHFR complexed with NADPH and iclaprim

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

Entity ID: 1

Experimental Data

Structure Validation

Deposition Data

Revision History