Cyclophilin A complexed with tri-vector ligand 4.

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors.

De Simone, A.Georgiou, C.Ioannidis, H.Gupta, A.A.Juarez-Jimenez, J.Doughty-Shenton, D.Blackburn, E.A.Wear, M.A.Richards, J.P.Barlow, P.N.Carragher, N.Walkinshaw, M.D.Hulme, A.N.Michel, J.

(2019) Chem Sci 10: 542-547

  • DOI: https://doi.org/10.1039/c8sc03831g
  • Primary Citation of Related Structures:  
    6GJI, 6GJJ, 6GJL, 6GJM, 6GJN, 6GJP, 6GJR, 6GJY

  • PubMed Abstract: 

    Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design.

  • Organizational Affiliation

    University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK . Email: mail@julienmichel.net.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A165Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L36

Download Ideal Coordinates CCD File 
B [auth A]ethyl 2-[[(4-aminophenyl)methyl-propyl-carbamoyl]amino]ethanoate
C15 H23 N3 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.726α = 90
b = 54.378β = 90
c = 87.283γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomNo. 336289

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description