4L0L

Crystal structure of P.aeruginosa PBP3 in complex with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Pyridone-conjugated monobactam antibiotics with gram-negative activity.

Brown, M.F.Mitton-Fry, M.J.Arcari, J.T.Barham, R.Casavant, J.Gerstenberger, B.S.Han, S.Hardink, J.R.Harris, T.M.Hoang, T.Huband, M.D.Lall, M.S.Lemmon, M.M.Li, C.Lin, J.McCurdy, S.P.McElroy, E.McPherson, C.Marr, E.S.Mueller, J.P.Mullins, L.Nikitenko, A.A.Noe, M.C.Penzien, J.Plummer, M.S.Schuff, B.P.Shanmugasundaram, V.Starr, J.T.Sun, J.Tomaras, A.Young, J.A.Zaniewski, R.P.

(2013) J Med Chem 56: 5541-5552

  • DOI: https://doi.org/10.1021/jm400560z
  • Primary Citation of Related Structures:  
    4L0L

  • PubMed Abstract: 

    Herein we describe the structure-aided design and synthesis of a series of pyridone-conjugated monobactam analogues with in vitro antibacterial activity against clinically relevant Gram-negative species including Pseudomonas aeruginosa , Klebsiella pneumoniae , and Escherichia coli . Rat pharmacokinetic studies with compound 17 demonstrate low clearance and low plasma protein binding. In addition, evidence is provided for a number of analogues suggesting that the siderophore receptors PiuA and PirA play a role in drug uptake in P. aeruginosa strain PAO1.


  • Organizational Affiliation

    Worldwide Medicinal Chemistry, ‡Computational Chemistry, §Antibacterials Research Unit, ∥Pharmacokinetics, Dynamics & Metabolism, ⊥Structural Biology, Pfizer Global Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 3537Pseudomonas aeruginosaMutation(s): 0 
Gene Names: pbpB
UniProt
Find proteins for Q51504 (Pseudomonas aeruginosa)
Explore Q51504 
Go to UniProtKB:  Q51504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51504
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PFV
Query on PFV

Download Ideal Coordinates CCD File 
B [auth A](6R,7S,10Z)-10-(2-amino-1,3-thiazol-4-yl)-1-(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)-7-formyl-13,13-dimethyl-3,9-dioxo-6-(sulfoamino)-12-oxa-2,4,8,11-tetraazatetradec-10-en-14-oic acid
C20 H26 N8 O12 S2
DRGQACYRFXBYPT-SATPWBBZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PFV PDBBind:  4L0L IC50: 54 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.725α = 90
b = 82.832β = 90
c = 88.689γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references