Co-Crystal structure of P. aeruginosa LpxC-achn975 complex

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Optimization of LpxC Inhibitors for Antibacterial Activity and Cardiovascular Safety.

Cohen, F.Aggen, J.B.Andrews, L.D.Assar, Z.Boggs, J.Choi, T.Dozzo, P.Easterday, A.N.Haglund, C.M.Hildebrandt, D.J.Holt, M.C.Joly, K.Jubb, A.Kamal, Z.Kane, T.R.Konradi, A.W.Krause, K.M.Linsell, M.S.Machajewski, T.D.Miroshnikova, O.Moser, H.E.Nieto, V.Phan, T.Plato, C.Serio, A.W.Seroogy, J.Shakhmin, A.Stein, A.J.Sun, A.D.Sviridov, S.Wang, Z.Wlasichuk, K.Yang, W.Zhou, X.Zhu, H.Cirz, R.T.

(2019) ChemMedChem 14: 1560-1572

  • DOI: https://doi.org/10.1002/cmdc.201900287
  • Primary Citation of Related Structures:  
    6MO4, 6MO5, 6MOD, 6MOO

  • PubMed Abstract: 

    UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a Zn 2+ deacetylase that is essential for the survival of most pathogenic Gram-negative bacteria. ACHN-975 (N-((S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl)-4-(((1R,2R)-2-(hydroxymethyl)cyclopropyl)buta-1,3-diyn-1-yl)benzamide) was the first LpxC inhibitor to reach human clinical testing and was discovered to have a dose-limiting cardiovascular toxicity of transient hypotension without compensatory tachycardia. Herein we report the effort beyond ACHN-975 to discover LpxC inhibitors optimized for enzyme potency, antibacterial activity, pharmacokinetics, and cardiovascular safety. Based on its overall profile, compound 26 (LPXC-516, (S)-N-(2-(hydroxyamino)-1-(3-methoxy-1,1-dioxidothietan-3-yl)-2-oxoethyl)-4-(6-hydroxyhexa-1,3-diyn-1-yl)benzamide) was chosen for further development. A phosphate prodrug of 26 was developed that provided a solubility of >30 mg mL -1 for parenteral administration and conversion into the active drug with a t 1/2 of approximately two minutes. Unexpectedly, and despite our optimization efforts, the prodrug of 26 still possesses a therapeutic window insufficient to support further clinical development.

  • Organizational Affiliation

    Achaogen Inc., 1 Tower Place, Suite 400, South San Francisco, CA, 94080, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase305Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P47205 
Go to UniProtKB:  P47205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on A5F

Download Ideal Coordinates CCD File 
C [auth A]N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide
C20 H23 N3 O4
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
A5F Binding MOAD:  6MOO IC50: 19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.887α = 90
b = 66.86β = 90.81
c = 63.728γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary