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

  • Resolution: 2.41 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1038/s41586-018-0483-6
  • Primary Citation of Related Structures:  

  • 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 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 Infectious Diseases, Genentech, South San Francisco, CA, USA. smith.peter@gene.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal peptidase I
A, B
247Escherichia coli K-12Mutation(s): 0 
Gene Names: lepBb2568JW2552
Find proteins for P00803 (Escherichia coli (strain K12))
Explore P00803 
Go to UniProtKB:  P00803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00803
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CZD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C47 H61 N11 O7
Query on 1PE

Download Ideal Coordinates CCD File 
C10 H22 O6
Experimental Data & Validation

Experimental Data

  • 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
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description