6B88

E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Optimized arylomycins are a new class of Gram-negative antibiotics.

Smith, P.A.Koehler, M.F.T.Girgis, H.S.Yan, D.Chen, Y.Chen, Y.Crawford, J.J.Durk, M.R.Higuchi, R.I.Kang, J.Murray, J.Paraselli, P.Park, S.Phung, W.Quinn, J.G.Roberts, T.C.Rouge, L.Schwarz, J.B.Skippington, E.Wai, J.Xu, M.Yu, Z.Zhang, H.Tan, M.W.Heise, C.E.

(2018) Nature 561: 189-194

  • DOI: 10.1038/s41586-018-0483-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts no new class of antibiotic with activity against Gram-negative bacteria has been approved in over fifty years. Natural products and their derivatives have a k ...

    Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts no new class of antibiotic with activity against Gram-negative bacteria has been approved in over fifty years. Natural products and their derivatives have a key role in combating Gram-negative pathogens. Here we report chemical optimization of the arylomycins-a class of natural products with weak activity and limited spectrum-to obtain G0775, a molecule with potent, broad-spectrum activity against Gram-negative bacteria. G0775 inhibits the essential bacterial type I signal peptidase, a new antibiotic target, through an unprecedented molecular mechanism. It circumvents existing antibiotic resistance mechanisms and retains activity against contemporary multidrug-resistant Gram-negative clinical isolates in vitro and in several in vivo infection models. These findings demonstrate that optimized arylomycin analogues such as G0775 could translate into new therapies to address the growing threat of multidrug-resistant Gram-negative infections.


    Organizational Affiliation

    Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA. heise.christopher@gene.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Signal peptidase I
A, B
247Escherichia coli K-12Mutation(s): 0 
Gene Names: lepBb2568JW2552
EC: 3.4.21.89
Find proteins for P00803 (Escherichia coli (strain K12))
Go to UniProtKB:  P00803
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZD
Query on CZD

Download CCD File 
A, B
(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide
C47 H61 N11 O7
SJYWASAPFZIDQL-UAKBWTGGSA-N
 Ligand Interaction
1PE
Query on 1PE

Download CCD File 
B
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.98α = 90
b = 109.98β = 90
c = 116.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references, Structure summary