6XBE

Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1.

Mulligan, V.K.Workman, S.Sun, T.Rettie, S.Li, X.Worrall, L.J.Craven, T.W.King, D.T.Hosseinzadeh, P.Watkins, A.M.Renfrew, P.D.Guffy, S.Labonte, J.W.Moretti, R.Bonneau, R.Strynadka, N.C.J.Baker, D.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2012800118
  • Primary Citation of Related Structures:  
    6XBF, 6XCI, 6XBE

  • PubMed Abstract: 
  • The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l- and d-amino acids that are able to bind to and inhibit targets of therapeutic interest ...

    The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l- and d-amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC 50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.


    Organizational Affiliation

    Institute for Protein Design, Department of Biochemistry, Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BlaNDM-4_1_JQ348841 ABCD248Klebsiella pneumoniaeMutation(s): 0 
Gene Names: 
Find proteins for E9NWK5 (Klebsiella pneumoniae)
Explore E9NWK5 
Go to UniProtKB:  E9NWK5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
macrocycle inhibitor NDM1i-1F FGHI8synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002397
Query on PRD_002397
F, G, H, ICyclic peptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.699α = 96.52
b = 74.551β = 103.11
c = 77.31γ = 106.24
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release