6B88 | pdb_00006b88

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)

• PDB DOI: https://doi.org/10.2210/pdb6B88/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-05 Released: 2018-10-10 
• Deposition Author(s): Murray, J.M., Rouge, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.265 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

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

• PubMed: 30209367 
• DOI: https://doi.org/10.1038/s41586-018-0483-6
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Infectious Diseases, Genentech, South San Francisco, CA, USA. [e-mail].
Department of Discovery Chemistry, Genentech, South San Francisco, CA, USA.
Department of Infectious Diseases, Genentech, South San Francisco, CA, USA.
Department of Translational Immunology, Genentech, South San Francisco, CA, USA.
Department of Chemistry, Wuxi AppTec, Shanghai, China.
Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA.
RQx Pharmaceuticals, La Jolla, CA, USA.
Retrovirox, San Diego, CA, USA.
Department of Structural Biology, Genentech, South San Francisco, CA, USA.
Vertex, San Diego, CA, USA.
Department of Microchem Proteomics, Genentech, South San Francisco, CA, USA.
Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA.
Aduro Biotech, Berkeley, CA, USA.
FLX Bio, South San Francisco, CA, USA.
Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.
Department of Infectious Diseases, Genentech, South San Francisco, CA, USA. [e-mail].
Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.5 kDa 
• Atom Count: 3,947 
• Modeled Residue Count: 479 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase I	A, B	247	Escherichia coli K-12	Mutation(s): 0  Gene Names: lepB, b2568, JW2552 EC: 3.4.21.89
UniProt
Find proteins for P00803 (Escherichia coli (strain K12)) Explore P00803  Go to UniProtKB:  P00803

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CZD	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	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 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.98	α = 90
b = 109.98	β = 90
c = 116.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Murray, J.M., Rouge, L.

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Structure summary