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 ...

    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 CCD File 
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 CCD File 
A
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
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



Entry History 

Deposition Data

Revision History 

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