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


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41586-018-0483-6
  • Primary Citation of Related Structures:  
    6B88

  • 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.


Macromolecules
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
EC: 3.4.21.89
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CZD
Query on CZD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth 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
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
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



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