Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 20118.69 
• Atom Count: 1416 
• Residue Count: 163 
• Unique protein chains: 1

4FGG

S. aureus dihydrofolate reductase co-crystallized with propyl-DAP isobutenyl-dihydrophthalazine inhibitor

• DOI: 10.2210/pdb4FGG/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-06-04 Released: 2013-01-09 
• Deposition Author(s): Bourne, C.R., Barrow, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 

Literature

Inhibition of Bacterial Dihydrofolate Reductase by 6-Alkyl-2,4-diaminopyrimidines.

Nammalwar, B., Bourne, C.R., Bunce, R.A., Wakeham, N., Bourne, P.C., Ramnarayan, K., Mylvaganam, S., Berlin, K.D., Barrow, E.W., Barrow, W.W.

(2012) Chemmedchem 7: 1974-1982

• PubMed: 22930550 
• DOI: 10.1002/cmdc.201200291
• Primary Citation of Related Structures:  
  4FGH


• PubMed Abstract: 
  

(±)-6-Alkyl-2,4-diaminopyrimidine-based inhibitors of bacterial dihydrofolate reductase (DHFR) have been prepared and evaluated for biological potency against Bacillus anthracis and Staphylococcus aureus. Biological studies revealed attenuated activity relative to earlier structures lacking substitution at C6 of the diaminopyrimidine moiety, though minimum inhibitory concentration (MIC) values are in the 0.125-8 μg mL(-1) range for both organisms. This effect was rationalized from three- dimensional X-ray structure studies that indicate the presence of a side pocket containing two water molecules adjacent to the main binding pocket. Because of the hydrophobic nature of the substitutions at C6, the main interactions are with protein residues Leu 20 and Leu 28. These interactions lead to a minor conformational change in the protein, which opens the pocket containing these water molecules such that it becomes continuous with the main binding pocket. These water molecules are reported to play a critical role in the catalytic reaction, highlighting a new area for inhibitor expansion within the limited architectural variation at the catalytic site of bacterial DHFR.

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Organizational Affiliation: 

Department of Chemistry, Oklahoma State University, Stillwater, OK 74078 (USA).

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrofolate reductase	A	163	Staphylococcus aureus	Mutation(s): 0  Gene Names: folA EC: 1.5.1.3
Find proteins for P0A017 (Staphylococcus aureus) Go to UniProtKB:  P0A017

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
0U5	A	(2E)-3-{5-[(2,4-diamino-6-propylpyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}-1-[(1S)-1-(2-methylprop-1-en-1-yl)phthalazin-2(1H)-yl]prop-2-en-1-one C31 H36 N6 O3 FJDNNCPVIFOVAR-JYSHFMIGSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0U5	Ki: 4.1 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.012	α = 90.00
b = 79.012	β = 90.00
c = 107.529	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-04 
• Released Date: 2013-01-09 
• Deposition Author(s): Bourne, C.R., Barrow, W.W.

Revision History 

• Version 1.0: 2013-01-09
  Type: Initial release
• Version 1.1: 2013-01-16
  Type: Database references
• Version 1.2: 2013-04-17
  Type: Database references
• Version 1.3: 2013-11-20
  Type: Database references