6MOD | pdb_00006mod

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

• PDB DOI: https://doi.org/10.2210/pdb6MOD/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2019-07-17 
• Deposition Author(s): Stein, A.J., Holt, M.C., Assar, Z., Cohen, F., Andrews, L., Cirz, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

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

• PubMed: 31283109 
• DOI: https://doi.org/10.1002/cmdc.201900287
• Primary Citation 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.

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Organizational Affiliation: 
• Achaogen Inc., 1 Tower Place, Suite 400, South San Francisco, CA, 94080, USA.
Cayman Chemical Co., 1180 East Ellsworth, Ann Arbor, MI, 48108, USA.
Plato BioPharma Inc., 7581 West 103rd Avenue, Unit 300, Westminster, CO, 80021, USA.
Nanosyn Inc., 3100 Central Expressway, Santa Clara, CA, 95051, USA.
Konradi Molecular, 30 Victoria Road, Burlingame, CA, 94010, USA.
Pharmaron Inc., 6 Tai-He Road, BDA, Beijing, 100176, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2,499 
• Modeled Residue Count: 298 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	304	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lpxC, PLES_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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JWV	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
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JWV	BindingDB:  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 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.079	α = 90
b = 66.911	β = 91.08
c = 63.462	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Stein, A.J., Holt, M.C., Assar, Z., Cohen, F., Andrews, L., Cirz, R.

Revision History  

• 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: 2024-03-13
  Changes: Data collection, Database references