6R8W

Human Cyclophilin D in complex with 2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.

Gradler, U.Schwarz, D.Blaesse, M.Leuthner, B.Johnson, T.L.Bernard, F.Jiang, X.Marx, A.Gilardone, M.Lemoine, H.Roche, D.Jorand-Lebrun, C.

(2019) Bioorg.Med.Chem.Lett. 29: 126717-126717

  • DOI: 10.1016/j.bmcl.2019.126717
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based screening by SPR enabled the discovery of chemical diverse fragment hits with millimolar binding affinities to the peptidyl-prolyl isomerase Cyclophilin D (CypD). The CypD protein crystal structures of 6 fragment hits provided the basi ...

    Fragment-based screening by SPR enabled the discovery of chemical diverse fragment hits with millimolar binding affinities to the peptidyl-prolyl isomerase Cyclophilin D (CypD). The CypD protein crystal structures of 6 fragment hits provided the basis for subsequent medicinal chemistry optimization by fragment merging and linking yielding three different chemical series with either urea, oxalyl or amide linkers connecting millimolar fragments in the S1' and S2 pockets. We successfully improved the in vitro CypD potencies in the biochemical FP and PPIase assays and in the biophysical SPR binding assay from millimolar towards the low micromolar and submicromolar range by >1000-fold for some fragment derivatives. The initial SAR together with the protein crystal structures of our novel CypD inhibitors provide a suitable basis for further hit-to-lead optimization.


    Organizational Affiliation

    Merck Healthcare, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: ulrich.graedler@merckgroup.com.,Proteros Biostructures GmbH, Bunsenstra├če 7a, D-82152 Planegg-Martinsried, Germany.,Merck Healthcare, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany.,Edelris, 115 Avenue, Lacassagne, F-69003 Lyon, France.,EMD Serono Research & Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A
164Homo sapiensMutation(s): 1 
Gene Names: PPIF (CYP3)
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Go to Gene View: PPIF
Go to UniProtKB:  P30405
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JVH
Query on JVH

Download SDF File 
Download CCD File 
A
2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide
C23 H27 N3 O5
BOGJVTQQRCPUBE-MZBUVPGESA-N
 Ligand Interaction
O4B
Query on O4B

Download SDF File 
Download CCD File 
A
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
C12 H24 O6
XEZNGIUYQVAUSS-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.099α = 90.00
b = 57.099β = 90.00
c = 116.073γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-04-02 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Graedler, U.

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release