3M08

Wild Type Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1

PDB DOI: 10.2210/pdb3M08/pdb

Classification: Oxidoreductase/Oxidoreductase inhibitor
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-03-02 Released: 2010-07-14
Deposition Author(s): Bourne, C.R., Barrow, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.213
R-Value Work: 0.175
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Inhibition of Antibiotic-Resistant Staphylococcus aureus by the Broad-Spectrum Dihydrofolate Reductase Inhibitor RAB1.

Bourne, C.R., Barrow, E.W., Bunce, R.A., Bourne, P.C., Berlin, K.D., Barrow, W.W.

(2010) Antimicrob Agents Chemother 54: 3825-3833

PubMed: 20606069 Search on PubMedSearch on PubMed Central
DOI: 10.1128/AAC.00361-10
Primary Citation of Related Structures:
3M08, 3M09

PubMed Abstract:

The bacterial burden on human health is quickly outweighing available therapeutics. Our long-term goal is the development of antimicrobials with the potential for broad-spectrum activity. We previously reported phthalazine-based inhibitors of dihydrofolate reductase (DHFR) with potent activity against Bacillus anthracis, a major component of Project BioShield. The most active molecule, named RAB1, performs well in vitro and, in a cocrystal structure, was found deep within the active site of B. anthracis DHFR. We have now examined the activity of RAB1 against a panel of bacteria relevant to human health and found broad-spectrum applicability, particularly with regard to gram-positive organisms. RAB1 was most effective against Staphylococcus aureus, including methicillin- and vancomycin-resistant (MRSA/VRSA) strains. We have determined the cocrystal structure of the wild-type and trimethoprim-resistant (Phe 98 Tyr) DHFR enzyme from S. aureus with RAB1, and we found that rotational freedom of the acryloyl linker region allows the phthalazine moiety to occupy two conformations. This freedom in placement also allows either enantiomer of RAB1 to bind to S. aureus, in contrast to the specificity of B. anthracis for the S-enantiomer. Additionally, one of the conformations of RAB1 defines a unique surface cavity that increases the strength of interaction with S. aureus. These observations provide insights into the binding capacity of S. aureus DHFR and highlight atypical features critical for future exploitation in drug development.

Related Citations:

Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity
Bourne, C.R., Bunce, R.A., Bourne, P.C., Berlin, K.D., Barrow, E.W., Barrow, W.W.
(2009) Antimicrob Agents Chemother 53: 3065

Organizational Affiliation:

Department of Veterinary Pathobiology, 250 McElroy Hall, Oklahoma State University, Stillwater, OK 74078, USA. christina.bourne@okstate.edu

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	161	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A017
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
RAR Query on RAR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine C₂₇ H₃₀ N₆ O₃ YGDVMSPWZQHNMB-NEQMZLFVSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
RAR	Binding MOAD: 3M08	Ki: 2.8 (nM) from 1 assay(s)
	BindingDB: 3M08	Ki: 0.9 (nM) from 1 assay(s)
	BindingDB: 3M08	IC50: min: 2.9, max: 12.5 (nM) from 2 assay(s)