5KH5 | pdb_00005kh5

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

• PDB DOI: https://doi.org/10.2210/pdb5KH5/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.274 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

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

• PubMed: 27379833 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00746
• Primary Citation Related Structures: 
  5KH2, 5KH4, 5KH5


• 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. 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.

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Organizational Affiliation: 
• GlaxoSmithKline , 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States.
GlaxoSmithKline , 830 Winter Street, Waltham, Massachusetts 02451, United States.
GlaxoSmithKline , 5 Moore Drive, Research Triangle Park, North Carolina 27009, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.38 kDa 
• Atom Count: 3,633 
• Modeled Residue Count: 455 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoprenyl transferase	A, B	272	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: uppS, SP_0261 EC: 2.5.1
UniProt
Find proteins for Q97SR4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97SR4  Go to UniProtKB:  Q97SR4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6TC	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.274 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.451	α = 90
b = 117.911	β = 90
c = 179.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations