5KX2

NMR Solution Structure of Designed Peptide NC_cEE_D1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Accurate de novo design of hyperstable constrained peptides.

Bhardwaj, G.Mulligan, V.K.Bahl, C.D.Gilmore, J.M.Harvey, P.J.Cheneval, O.Buchko, G.W.Pulavarti, S.V.Kaas, Q.Eletsky, A.Huang, P.S.Johnsen, W.A.Greisen, P.J.Rocklin, G.J.Song, Y.Linsky, T.W.Watkins, A.Rettie, S.A.Xu, X.Carter, L.P.Bonneau, R.Olson, J.M.Coutsias, E.Correnti, C.E.Szyperski, T.Craik, D.J.Baker, D.

(2016) Nature 538: 329-335

  • DOI: 10.1038/nature19791
  • Primary Citation of Related Structures:  
    2ND3, 2ND2, 5JG9, 5JHI, 5JI4, 5KVN, 5KWZ, 5KX2, 5KWX, 5KWP, 5KX1, 5KWO, 5KX0

  • PubMed Abstract: 
  • Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics ...

    Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Designed peptide NC_cEE_D1A18synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5KX2 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2016-11-02
    Changes: Database references
  • Version 1.3: 2019-10-30
    Changes: Data collection, Database references, Structure summary