6RMF

Crystal structure of NDM-1 with VNRX-5133


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases.

Krajnc, A.Brem, J.Hinchliffe, P.Calvopina, K.Panduwawala, T.Lang, P.A.Kamps, J.J.A.G.Tyrell, J.M.Widlake, E.Saward, B.G.Walsh, T.R.Spencer, J.Schofield, C.J.

(2019) J.Med.Chem. --: --

  • DOI: 10.1021/acs.jmedchem.9b00911
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bicyclic boronate VNRX-5133 is a new type of β-lactamase inhibitor in clinical development. We report that VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2. VNRX- ...

    The bicyclic boronate VNRX-5133 is a new type of β-lactamase inhibitor in clinical development. We report that VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2. VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not observed. Crystallography reveals how VNRX-5133 binds to the class D SBL OXA-10 and NDM-1. The crystallographic results highlight the ability of bicyclic boronates to inhibit SBLs and MBLs via binding of a tetrahedral (sp3) boron species. The structures imply conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1, by crystallography we observed an unanticipated VNRX-5133 binding mode involving cyclization of its acylamino oxygen onto the boron of the bicyclic core. Different side-chain-dependent binding modes for bicyclic boronates imply scope for optimisation. The results further support the 'high energy intermediate' analogue approach for broad-spectrum β-lactamase inhibitor development and highlight the ability of boron-inhibitors to interchange between different hybridization states / binding modes.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A, B
244Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Go to UniProtKB:  C7C422
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K9K
Query on K9K

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A, B
5-[[4-(2-azanylethylamino)cyclohexyl]methyl]-3-oxidanyl-2,4-dioxa-6-aza-3$l^{4}-boratricyclo[7.4.0.0^{3,7}]trideca-1(13),5,9,11-tetraene-13-carboxylic acid
C19 H27 B N3 O5
OFJWWODZZUVYKK-NOLJZWGESA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
K9B
Query on K9B

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A
3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2,2-bis(oxidanyl)-3,4-dihydro-1,2$l^{4}-benzoxaborinine-8-carboxylic acid
C19 H29 B N3 O6
PQJIZCXMKLVZCE-NOLJZWGESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.821α = 90.00
b = 73.837β = 90.00
c = 77.681γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release