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 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
Binding Affinity Annotations 
IDSourceBinding Affinity
TH9 PDBBind:  3TH8 IC50: 560 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 
  • 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 


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