Crystal Structure of IMP-1 metallo-beta-lactamase complexed with a 3-aminophtalic acid inhibitor

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

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X-ray crystallographic analysis of IMP-1 metallo-beta-lactamase complexed with a 3-aminophthalic acid derivative, structure-based drug design, and synthesis of 3,6-disubstituted phthalic acid derivative inhibitors

Hiraiwa, Y.Saito, J.Watanabe, T.Yamada, M.Morinaka, A.Fukushima, T.Kudo, T.

(2014) Bioorg Med Chem Lett 24: 4891-4894

  • DOI: https://doi.org/10.1016/j.bmcl.2014.08.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    3-(4-Hydroxypiperidine-1-yl) phthalic acid 1 shows potent inhibitory activity against metallo-β-lactamase, which is known to inactivate β-lactam antibiotics such as carbapenems. Here, the structure of co-crystals of the metallo-β-lactamase IMP-1 and 1 was first analyzed by X-ray crystallography, and then used for structure-based drug design. Four novel compounds bearing substituents at the 6-position were synthesized to produce 3,6-disubstituted phthalic acid derivatives, and their IMP-1 inhibitory activity and synergistic effect with the carbapenem biapenem (BIPM) were evaluated. 3,6-Disubstituted phthalic acid derivatives showed potent IMP-1 inhibitory activity. In particular, compound 13 showed 10-fold higher IMP-1 inhibitory activity as compared with the parent derivative 1.

  • Organizational Affiliation

    Pharmaceutical Research Center, Meiji Seika Pharma, Co., Ltd, 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
222Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaIMP-1bla IMPbla-impblaESPimp
Find proteins for Q79MP6 (Pseudomonas aeruginosa)
Explore Q79MP6 
Go to UniProtKB:  Q79MP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79MP6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.994α = 90
b = 52.795β = 90
c = 198.384γ = 90
Software Package:
Software NamePurpose
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release