5KH5

Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS) IN COMPLEX WITH ~{N}-(3-azanyl-3-oxidanylidene-propyl)-5-(1-benzothiophen-5-yl)-1-(phenylmethyl)-~{N}-[(4-propan-2-yloxyphenyl)methyl]pyrazole-4-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase.

Concha, N.Huang, J.Bai, X.Benowitz, A.Brady, P.Grady, L.C.Kryn, L.H.Holmes, D.Ingraham, K.Jin, Q.Pothier Kaushansky, L.McCloskey, L.Messer, J.A.O'Keefe, H.Patel, A.Satz, A.L.Sinnamon, R.H.Schneck, J.Skinner, S.R.Summerfield, J.Taylor, A.Taylor, J.D.Evindar, G.Stavenger, R.A.

(2016) J Med Chem 59: 7299-7304

  • DOI: 10.1021/acs.jmedchem.6b00746
  • Primary Citation of Related Structures:  
    5KH2, 5KH5, 5KH4

  • PubMed Abstract: 
  • Undecaprenyl pyrophosphate synthase (UppS) is an essential enzyme in bacterial cell wall synthesis. Here we report the discovery of Staphylococcus aureus UppS inhibitors from an Encoded Library Technology screen and demonstrate binding to the hydrophobic substrate site through cocrystallography studies ...

    Undecaprenyl pyrophosphate synthase (UppS) is an essential enzyme in bacterial cell wall synthesis. Here we report the discovery of Staphylococcus aureus UppS inhibitors from an Encoded Library Technology screen and demonstrate binding to the hydrophobic substrate site through cocrystallography studies. The use of bacterial strains with regulated uppS expression and inhibitor resistant mutant studies confirmed that the whole cell activity was the result of UppS inhibition, validating UppS as a druggable antibacterial target.


    Organizational Affiliation

    GlaxoSmithKline , 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoprenyl transferaseA, B272Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: uppSSP_0261
EC: 2.5.1
Find proteins for Q97SR4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q97SR4 
Go to UniProtKB:  Q97SR4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6TC
Query on 6TC

Download Ideal Coordinates CCD File 
C [auth B]~{N}-(3-azanyl-3-oxidanylidene-propyl)-5-(1-benzothiophen-5-yl)-1-(phenylmethyl)-~{N}-[(4-propan-2-yloxyphenyl)methyl]pyrazole-4-carboxamide
C32 H32 N4 O3 S
YEDMOKVDDMHGJC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.451α = 90
b = 117.911β = 90
c = 179.693γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-06-14 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Concha, N.O.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references