6GJN

Cyclophilin A complexed with tri-vector ligand 15.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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
  • Structures With Same Primary Citation

  • 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

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



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: PPIACYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F0Q
Query on F0Q

Download CCD File 
A
1-[(4-aminophenyl)methyl]-3-[2-[(2~{R})-2-(2-bromophenyl)pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-1-[(2-methyl-1,2,3,4-tetrazol-5-yl)methyl]urea
C23 H27 Br N8 O2
DZZMUGFFAZZVFF-HXUWFJFHSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.952α = 90
b = 53.348β = 90
c = 88.898γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references