28KD | pdb_000028kd

ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Yeast Display Technology Enables Rapid Discovery of Low-Nanomolar Macrocyclic Peptide Inhibitors of Human Angiotensin-Converting Enzyme 2.

Romanyuk, Z.Bettin, G.Brear, P.Linciano, S.Mazzocato, Y.Bonadies, S.Zanotto, I.Mazzucco, C.Monferone, A.Soler, M.A.Pasut, G.Martin, S.Scarso, A.Heinis, C.Rothenberger, S.Hyvonen, M.Angelini, A.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02876
  • Primary Citation Related Structures: 
    28KD, 9RVT, 9SPA

  • PubMed Abstract: 

    Macrocyclic peptides (MPs) are valuable molecular formats for drug development, bridging small molecules and larger biologics due to their favorable pharmacological properties. Here, we describe the discovery of low-nanomolar inhibitors of human angiotensin-converting enzyme 2 (hACE2) by quantitatively screening millions of structurally diverse disulfide-cyclized peptide ligands using yeast display technology. The most potent yeast-encoded "one-ring" and "two-ring" MP inhibit hACE2 with K i values of 1.9 and 1.5 nM, respectively. These inhibitory potencies are comparable to those of other cyclic peptides discovered using well-established in vitro display technologies. Crystal structures of the two MPs in complex with hACE2 reveal the adoption of either a rigid β-hairpin or a cysteine-stabilized α-helix/α-helix motif. Both MPs exhibit binding modes distinct from those of previously reported inhibitors. Thus, yeast display is a valid technology to rapidly generate MPs with desired binding properties for the development of potential therapeutics.


  • Organizational Affiliation
    • Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Processed angiotensin-converting enzyme 2A [auth B],
C [auth A]
609Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-CYS-PHE-LEU-ARG-CYS-HIS-ARG-ASP-VAL-LYS-CYS-TRP-LEU-TRP-CYS-SER-GLYB [auth C],
D
18Synthetic plasmidMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.257α = 90
b = 77.816β = 100.82
c = 115.179γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-08
    Type: Initial release