4U3D

LpxC from A.Aaeolicus in complex with 4-[[4-[2-[4-(morpholinomethyl)phenyl]ethynyl]phenoxy]methyl]tetrahydropyran-4-carbohydroxamic acid (compound 9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors.

Murphy-Benenato, K.E.Olivier, N.Choy, A.Ross, P.L.Miller, M.D.Thresher, J.Gao, N.Hale, M.R.

(2014) ACS Med Chem Lett 5: 1213-1218

  • DOI: 10.1021/ml500210x
  • Primary Citation of Related Structures:  
    4U3B, 4U3D

  • PubMed Abstract: 
  • In the search for novel Gram-negative agents, we performed a comprehensive search of the AstraZeneca collection and identified a tetrahydropyran-based matrix metalloprotease (MMP) inhibitor that demonstrated nanomolar inhibition of UDP-3-O-(acyl)-N-acetylglucosamine deacetylase (LpxC) ...

    In the search for novel Gram-negative agents, we performed a comprehensive search of the AstraZeneca collection and identified a tetrahydropyran-based matrix metalloprotease (MMP) inhibitor that demonstrated nanomolar inhibition of UDP-3-O-(acyl)-N-acetylglucosamine deacetylase (LpxC). Crystallographic studies in Aquifex aeolicus LpxC indicated the tetrahydropyran engaged in the same hydrogen bonds and van der Waals interactions as other known inhibitors. Systematic optimization of three locales on the scaffold provided compounds with improved Gram-negative activity. However, the optimization of LpxC activity was not accompanied by reduced inhibition of MMPs. Comparison of the crystal structure of the native product, UDP-3-O-(acyl)-glucosamine, in Aquifex aeolicus to the structure of a tetrahydropyran-based inhibitor indicates pathways for future optimization.


    Organizational Affiliation

    Department of Chemistry, Infection Innovative Medicines, and Discovery Sciences, AstraZeneca R&D, Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseA271Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: lpxCenvAaq_1772
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5))
Explore O67648 
Go to UniProtKB:  O67648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67648
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BX
Query on 3BX

Download Ideal Coordinates CCD File 
F [auth A]N-hydroxy-4-[(4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}phenoxy)methyl]tetrahydro-2H-pyran-4-carboxamide
C26 H30 N2 O5
RGQLOHCHGMQBNF-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.865α = 90
b = 65.865β = 90
c = 133.282γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references