Crystal structure of UPPs in complex with FPP and an allosteric inhibitor

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase.

Danley, D.E.Baima, E.T.Mansour, M.Fennell, K.F.Chrunyk, B.A.Mueller, J.P.Liu, S.Qiu, X.

(2015) Protein Sci 24: 20-26

  • DOI: https://doi.org/10.1002/pro.2579
  • Primary Citation of Related Structures:  
    4Q9M, 4Q9O

  • PubMed Abstract: 

    Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC50 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC90 0.4 µg mL(-1) ). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.

  • Organizational Affiliation

    Worldwide Research and Development, Pfizer Inc, Groton, Connecticut, 06340.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoprenyl transferase
A, B
246Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: uppSspr0240
EC: 2.5.1
Find proteins for Q8DRB3 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DRB3 
Go to UniProtKB:  Q8DRB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DRB3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FPP

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B]
C15 H28 O7 P2
Query on 2ZW

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
C20 H19 Cl N2 O2
Query on CD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
2ZW Binding MOAD:  4Q9M Kd: 66 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.85α = 90
b = 91.85β = 90
c = 155.54γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations