5MTF

A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
190Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: glpG
EC: 3.4.21.105
Find proteins for B7MDQ0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MDQ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
inhibitor
C
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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
W6Q
Query on W6Q
C
NON-POLYMERC13 H20 N2 O2

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ACE
Query on ACE
C
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.365α = 90.00
b = 111.365β = 90.00
c = 124.539γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy