6GJM

Cyclophilin A complexed with tri-vector ligand 4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.354 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1039/c8sc03831g
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Edinburgh Phenotypic Assay Centre , University of Edinburgh , Queen's Medical Research Institute , Little France Cres , Edinburgh , Scotland EH16 4TJ , UK.,The Edinburgh Protein Production Facility (EPPF) , University of Edinburgh , Level 3 Michael Swann Building, King's Buildings, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK.,Cancer Research UK Edinburgh Centre , University of Edinburgh , MRC Institute of Genetics and Molecular Medicine , Crewe Road South , Edinburgh , Scotland EH4 2XR , UK.,University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK . Email: mail@julienmichel.net.,University of Edinburgh , Michael Swann Building, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase A
A
165Homo sapiensMutation(s): 0 
Gene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L36
Query on L36

Download SDF File 
Download CCD File 
A
ethyl 2-[[(4-aminophenyl)methyl-propyl-carbamoyl]amino]ethanoate
C15 H23 N3 O3
KHLQRJYGXHCNMH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.354 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.726α = 90.00
b = 54.378β = 90.00
c = 87.283γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomNo. 336289

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references