4OON

Crystal structure of PBP1a in complex with compound 17 ((4Z,8S,11E,14S)-5-(2-amino-1,3-thiazol-4-yl)-14-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-8-formyl-2-methyl-6-oxo-3,10-dioxa-4,7,11-triazatetradeca-4,11-diene-2,12,14-tricarboxylic acid)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Literature

Siderophore receptor-mediated uptake of lactivicin analogues in gram-negative bacteria.

Starr, J., Brown, M.F., Aschenbrenner, L., Caspers, N., Che, Y., Gerstenberger, B.S., Huband, M., Knafels, J.D., Lemmon, M.M., Li, C., McCurdy, S.P., McElroy, E., Rauckhorst, M.R., Tomaras, A.P., Young, J.A., Zaniewski, R.P., Shanmugasundaram, V., Han, S.

(2014) J Med Chem 57: 3845-3855

  • DOI: 10.1021/jm500219c
  • Primary Citation of Related Structures:  
    4OOL, 4OOM, 4OON

  • PubMed Abstract: 

    • Multidrug-resistant Gram-negative pathogens are an emerging threat to human health, and addressing this challenge will require development of new antibacterial agents. This can be achieved through an improved molecular understanding of drug-target interactions combined with enhanced delivery of these agents to the site of action ...

    Multidrug-resistant Gram-negative pathogens are an emerging threat to human health, and addressing this challenge will require development of new antibacterial agents. This can be achieved through an improved molecular understanding of drug-target interactions combined with enhanced delivery of these agents to the site of action. Herein we describe the first application of siderophore receptor-mediated drug uptake of lactivicin analogues as a strategy that enables the development of novel antibacterial agents against clinically relevant Gram-negative bacteria. We report the first crystal structures of several sideromimic conjugated compounds bound to penicillin binding proteins PBP3 and PBP1a from Pseudomonas aeruginosa and characterize the reactivity of lactivicin and β-lactam core structures. Results from drug sensitivity studies with β-lactamase enzymes are presented, as well as a structure-based hypothesis to reduce susceptibility to this enzyme class. Finally, mechanistic studies demonstrating that sideromimic modification alters the drug uptake process are discussed.

    Organizational Affiliation: 

    Medicinal Chemistry, ⧧Computational Chemistry, §Antibacterials Research Unit, and ¶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
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein 1AA795Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: mrcA, ponA, PA5045
EC: 2.4.2 (PDB Primary Data), 3.4 (PDB Primary Data), 2.4.1.129 (UniProt), 3.4.16.4 (UniProt)
UniProt
Find proteins for Q07806 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q07806 
Go to UniProtKB:  Q07806
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07806
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2U4
Query on 2U4
Download Ideal Coordinates CCD File 
B [auth A](4Z,8S,11E,14S)-5-(2-amino-1,3-thiazol-4-yl)-14-(5,6-dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-8-formyl-2-methyl-6-oxo-3,10-dioxa-4,7,11-triazatetradeca-4,11-diene-2,12,14-tricarboxylic acid
C25 H24 N6 O14 S
VQOKWLNYKDCOTA-RCFVXGSMSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.77α = 90
b = 113.77β = 90
c = 123.46γ = 90
Software Package:
Software NamePurpose
AutoPROCdata collection
BUSTERrefinement
AutoPROCdata scaling
SCALAdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references