4C1F | pdb_00004c1f

Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers.

Brem, J.van Berkel, S.S.Zollman, D.Lee, S.Y.Gileadi, O.McHugh, P.J.Walsh, T.R.McDonough, M.A.Schofield, C.J.

(2015) Antimicrob Agents Chemother 60: 142-150

  • DOI: https://doi.org/10.1128/AAC.01335-15
  • Primary Citation Related Structures: 
    4BZ3, 4C09, 4C1C, 4C1D, 4C1E, 4C1F, 4C1G, 4C1H

  • PubMed Abstract: 

    β-Lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (MBLs). MBLs are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. Clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for MBLs. l-Captopril, which is used to treat hypertension via angiotensin-converting enzyme inhibition, has been reported to inhibit MBLs by chelating the active site zinc ions via its thiol(ate). We report systematic studies on B1 MBL inhibition by all four captopril stereoisomers. High-resolution crystal structures of three MBLs (IMP-1, BcII, and VIM-2) in complex with either the l- or d-captopril stereoisomer reveal correlations between the binding mode and inhibition potency. The results will be useful in the design of MBL inhibitors with the breadth of selectivity required for clinical application against carbapenem-resistant Enterobacteriaceae and other organisms causing MBL-mediated resistant infections.


  • Organizational Affiliation
    • Department of Chemistry, University of Oxford, Oxford, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 51.06 kDa 
  • Atom Count: 3,489 
  • Modeled Residue Count: 436 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-LACTAMASE IMP-1
A, B
228Serratia marcescensMutation(s): 0 
EC: 3.5.2.6 (PDB Primary Data), 3.1.26 (UniProt)
UniProt
Find proteins for P52699 (Serratia marcescens)
Explore P52699 
Go to UniProtKB:  P52699
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52699
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X8Z

Query on X8Z



Download:Ideal Coordinates CCD File
C [auth A]L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.62α = 90
b = 49.91β = 90
c = 54.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-09-17
    Changes: Other, Structure summary
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2016-01-13
    Changes: Database references
  • Version 1.4: 2018-02-21
    Changes: Database references, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description