Crystal structure of NDM-1 with VNRX-5133

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 3.0 of the entry. See complete history


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

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

(2019) J Med Chem 62: 8544-8556

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00911
  • Primary Citation of Related Structures:  
    6RMF, 6RTN

  • PubMed Abstract: 

    The bicyclic boronate VNRX-5133 (taniborbactam) 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 MBL NDM-1. The crystallographic results highlight the ability of bicyclic boronates to inhibit SBLs and MBLs via binding of a tetrahedral (sp 3 ) 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 binding modes for bicyclic boronates for SBLs and MBLs imply scope for side-chain optimization. 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.

  • Organizational Affiliation

    Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2
A, B
244Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K9B (Subject of Investigation/LOI)
Query on K9B

Download Ideal Coordinates CCD File 
I [auth A](4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
C19 H29 B N3 O6
K9K (Subject of Investigation/LOI)
Query on K9K

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
C19 H27 B N3 O5
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.821α = 90
b = 73.837β = 90
c = 77.681γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-30
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-05-13
    Changes: Derived calculations, Non-polymer description, Structure summary