4F6X

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

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 

wwPDB Validation   3D Report Full Report


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


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

  • 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 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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dehydrosqualene synthaseA292Staphylococcus aureusMutation(s): 0 
Gene Names: crtM
EC: 2.5.1.96
Find proteins for A9JQL9 (Staphylococcus aureus)
Explore A9JQL9 
Go to UniProtKB:  A9JQL9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZYL
Query on ZYL
Download Ideal Coordinates CCD File 
 B [auth A]1-[3-(hexyloxy)benzyl]-4-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxylic acid
C19 H23 N O5
IEFKPWNGVIDYEA-UHFFFAOYSA-N		 Ligand Interaction
TAR
Query on TAR
Download Ideal Coordinates CCD File 
 F [auth A]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A], E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZYLIC50:  45300   nM  Binding MOAD
ZYLIC50:  33000   nM  BindingDB
ZYLKi:  450   nM  BindingDB
ZYLIC50:  45300   nM  BindingDB
ZYLIC50 :  8200   nM  PDBBind
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 = 80.194α = 90
b = 80.194β = 90
c = 91.333γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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