3UHM

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pyridone methylsulfone hydroxamate LpxC inhibitors for the treatment of serious gram-negative infections.

Montgomery, J.I.Brown, M.F.Reilly, U.Price, L.M.Abramite, J.A.Arcari, J.Barham, R.Che, Y.Chen, J.M.Chung, S.W.Collantes, E.M.Desbonnet, C.Doroski, M.Doty, J.Engtrakul, J.J.Harris, T.M.Huband, M.Knafels, J.D.Leach, K.L.Liu, S.Marfat, A.McAllister, L.McElroy, E.Menard, C.A.Mitton-Fry, M.Mullins, L.Noe, M.C.O'Donnell, J.Oliver, R.Penzien, J.Plummer, M.Shanmugasundaram, V.Thoma, C.Tomaras, A.P.Uccello, D.P.Vaz, A.Wishka, D.G.

(2012) J Med Chem 55: 1662-1670

  • DOI: 10.1021/jm2014875
  • Primary Citation of Related Structures:  
    3UHM

  • PubMed Abstract: 
  • The synthesis and biological activity of a new series of LpxC inhibitors represented by pyridone methylsulfone hydroxamate 2a is presented. Members of this series have improved solubility and free fraction when compared to compounds in the previously described biphenyl methylsulfone hydroxamate series, and they maintain superior Gram-negative antibacterial activity to comparator agents ...

    The synthesis and biological activity of a new series of LpxC inhibitors represented by pyridone methylsulfone hydroxamate 2a is presented. Members of this series have improved solubility and free fraction when compared to compounds in the previously described biphenyl methylsulfone hydroxamate series, and they maintain superior Gram-negative antibacterial activity to comparator agents.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States. justin.montgomery@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseA299Pseudomonas aeruginosaMutation(s): 1 
Gene Names: lpxCenvAPA4406
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFN
Query on RFN

Download Ideal Coordinates CCD File 
C [auth A](2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide
C17 H20 N2 O5 S
NFQOWMXNJNMRTA-QGZVFWFLSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

Download Ideal Coordinates CCD File 
D [auth A]GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RFN Binding MOAD:  3UHM IC50: 3.6 (nM) from 1 assay(s)
PDBBind:  3UHM IC50: 3.6 (nM) from 1 assay(s)
BindingDB:  3UHM IC50: 3.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.138α = 90
b = 80.965β = 95.5
c = 49.779γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references