5MT6

Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-phenylethyl-ketoamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.

Ticha, A.Stanchev, S.Vinothkumar, K.R.Mikles, D.C.Pachl, P.Began, J.Skerle, J.Svehlova, K.Nguyen, M.T.N.Verhelst, S.H.L.Johnson, D.C.Bachovchin, D.A.Lepsik, M.Majer, P.Strisovsky, K.

(2017) Cell Chem Biol 24: 1523-1536.e4

  • DOI: 10.1016/j.chembiol.2017.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wid ...

    Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhomboid protease GlpG
A
180Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: glpG
EC: 3.4.21.105
Find proteins for P09391 (Escherichia coli (strain K12))
Go to UniProtKB:  P09391
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACE-ARG-VAL-ARG-HIS-ALA-V9C
B
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

Download SDF File 
Download CCD File 
A
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
V9C
Query on V9C
B
NON-POLYMERC9 H11 N O2

--

ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.710α = 90.00
b = 111.710β = 90.00
c = 124.229γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-06 
  • Released Date: 2017-11-15 
  • Deposition Author(s): Vinothkumar, K.R.

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references