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: 35.28 kDa 
• Atom Count: 2589 
• Modelled Residue Count: 281 
• Deposited Residue Count: 292 
• Unique protein chains: 1

4F6X

Crystal structure of dehydrosqualene synthase (crtm) from s. aureus complexed with bph-1112

• PDB DOI: 10.2210/pdb4F6X/pdb

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


• Deposited: 2012-05-15 Released: 2012-06-20 
• Deposition Author(s): Lin, F.-Y., Zhang, Y., Liu, Y.-L., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis.

Zhang, Y., Lin, F.-Y., Li, K., Zhu, W., Liu, Y.L., Cao, R., Pang, R., Lee, E., Axelson, J., Hensler, M., Wang, K., Molohon, K.J., Wang, Y., Mitchell, D.A., Nizet, V., Oldfield, E.

(2012) ACS Med Chem Lett 3: 402-406

• PubMed: 22662288 
• DOI: 10.1021/ml300038t
• Primary Citation of Related Structures:  
  3TH8, 4F6V, 4F6X


• PubMed Abstract: 
  

We report the discovery of antibacterial leads, keto- and diketo-acids, targeting two prenyl transferases: undecaprenyl diphosphate synthase (UPPS) and dehydrosqualene synthase (CrtM). The leads were suggested by the observation that keto- and diketo-acids bind to the active site Mg(2+)/Asp domain in HIV-1 integrase, and similar domains are present in prenyl transferases. We report the x-ray crystallographic structures of one diketo-acid and one keto-acid bound to CrtM, which supports the Mg(2+) binding hypothesis, together with the x-ray structure of one diketo-acid bound to UPPS. In all cases, the inhibitors bind to a farnesyl diphosphate substrate-binding site. Compound 45 had cell growth inhibition MIC(90) values of ~250-500 ng/mL against S. aureus, 500 ng/mL against Bacillus anthracis, 4 μg/mL against Listeria monocytogenes and Enterococcus faecium, and 1 μg/mL against Streptococcus pyogenes M1, but very little activity against E. coli (DH5α, K12) or human cell lines.

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Organizational Affiliation: 

PrenylX Research Institute, Zhangjiagang, 215600, P.R. China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrosqualene synthase	A	292	Staphylococcus aureus	Mutation(s): 0  Gene Names: crtM EC: 2.5.1.96
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus) Explore A9JQL9  Go to UniProtKB:  A9JQL9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZYL	B [auth A]	1-[3-(hexyloxy)benzyl]-4-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxylic acid C19 H23 N O5 IEFKPWNGVIDYEA-UHFFFAOYSA-N
TAR	F [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZYL	BindingDB:  4F6X	Ki: 450 (nM) from 1 assay(s)
		IC50: min: 3.30e+4, max: 4.53e+4 (nM) from 2 assay(s)
	PDBBind:  4F6X	IC50: 8200 (nM) from 1 assay(s)
	Binding MOAD:  4F6X	IC50: 4.53e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.238 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.194	α = 90
b = 80.194	β = 90
c = 91.333	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-15 
• Released Date: 2012-06-20 
Deposition Author(s): Lin, F.-Y., Zhang, Y., Liu, Y.-L., Oldfield, E.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Advisory, Database references