6MOD

Co-Crystal structure of P. aeruginosa LpxC-50432 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylaseA304Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lpxCPLES_47851
EC: 3.5.1.108
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JWV
Query on JWV

Download Ideal Coordinates CCD File 
C [auth A]N-[(1S)-2-(hydroxyamino)-1-(3-methoxy-1,1-dioxo-1lambda~6~-thietan-3-yl)-2-oxoethyl]-4-(6-hydroxyhexa-1,3-diyn-1-yl)benzamide
C19 H20 N2 O7 S
QVQHZORAUGAARX-MRXNPFEDSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JWV Binding MOAD:  6MOD IC50: 0.71 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.079α = 90
b = 66.911β = 91.08
c = 63.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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