4F6V

Crystal structure of dehydrosqualene synthase (crtm) from s. aureus complexed with bph-1034, mg2+ and fmp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZYMClick on this verticalbar to view detailsBest fitted FJPClick on this verticalbar to view detailsBest fitted SRTClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrosqualene synthase292Staphylococcus aureusMutation(s): 0 
Gene Names: crtM
EC: 2.5.1.96
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus)
Explore A9JQL9 
Go to UniProtKB:  A9JQL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9JQL9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZYM
Query on ZYM

Download Ideal Coordinates CCD File 
B [auth A]2,4-dioxo-4-{[3-(3-phenoxyphenyl)propyl]amino}butanoic acid
C19 H19 N O5
SJGQLSMZNBWNEL-UHFFFAOYSA-N
FJP
Query on FJP

Download Ideal Coordinates CCD File 
D [auth A](2E,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl dihydrogen phosphate
C15 H27 O4 P
ALEWCKXBHSDCCT-GNESMGCMSA-N
SRT
Query on SRT

Download Ideal Coordinates CCD File 
C [auth A]S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZYM BindingDB:  4F6V Ki: 250 (nM) from 1 assay(s)
IC50: min: 4000, max: 2.40e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.712α = 90
b = 80.712β = 90
c = 90.864γ = 120
Software Package:
Software NamePurpose
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZYMClick on this verticalbar to view detailsBest fitted FJPClick on this verticalbar to view detailsBest fitted SRTClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations