3TH8

Structure of E. coli undecaprenyl diphosphate synthase complexed with BPH-1063


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.309 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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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 TH9Click on this verticalbar to view details

This is version 1.2 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
Undecaprenyl pyrophosphate synthaseA [auth B],
B [auth A]
253Escherichia coli K-12Mutation(s): 0 
Gene Names: uppSispUrthyaeSb0174JW0169
EC: 2.5.1.31
UniProt
Find proteins for P60472 (Escherichia coli (strain K12))
Explore P60472 
Go to UniProtKB:  P60472
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60472
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TH9
Query on TH9

Download Ideal Coordinates CCD File 
C [auth B](2Z)-4-({3-[3-(hexyloxy)phenyl]propyl}amino)-2-hydroxy-4-oxobut-2-enoic acid
C19 H27 N O5
LTXZSLKTHFHDTP-VKAVYKQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.309 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.603α = 90
b = 68.862β = 90
c = 112.297γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

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 TH9Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description