6BEO

Solution structure of de novo macrocycle design9.1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Comprehensive computational design of ordered peptide macrocycles.

Hosseinzadeh, P.Bhardwaj, G.Mulligan, V.K.Shortridge, M.D.Craven, T.W.Pardo-Avila, F.Rettie, S.A.Kim, D.E.Silva, D.A.Ibrahim, Y.M.Webb, I.K.Cort, J.R.Adkins, J.N.Varani, G.Baker, D.

(2017) Science 358: 1461-1466

  • DOI: 10.1126/science.aap7577
  • Primary Citation of Related Structures:  6BEN, 6BER, 6BES, 6BET, 6BEU, 6BEW, 6BE7, 6BE9, 6BEQ, 6BF3, 6BF5

  • PubMed Abstract: 
  • Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide ...

    Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.


    Organizational Affiliation

    Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(DPR)PY(DHI)PKDL(DGN)
A
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DPR
Query on DPR
A
D-PEPTIDE LINKINGC5 H9 N O2

--

DHI
Query on DHI
A
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DGN
Query on DGN
A
D-PEPTIDE LINKINGC5 H10 N2 O3

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Department of Health & Human ServicesUnited States5R01GM103834

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release