4OC6

Structure of Cathepsin D with inhibitor 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based optimization of non-peptidic Cathepsin D inhibitors.

Gradler, U.Czodrowski, P.Tsaklakidis, C.Klein, M.Werkmann, D.Lindemann, S.Maskos, K.Leuthner, B.

(2014) Bioorg.Med.Chem.Lett. 24: 4141-4150

  • DOI: 10.1016/j.bmcl.2014.07.054
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency i ...

    We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay. However, the most potent analogues showed only micromolar activities in an ex vivo glycosaminoglycan (GAG) release assay in bovine cartilage together with low cellular permeability and suboptimal microsomal stability. This new scaffold can serve as a starting point for further optimization towards in vivo efficacy.


    Organizational Affiliation

    Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany. Electronic address: ulrich.graedler@merckgroup.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin D light chain
A
103Homo sapiensMutation(s): 0 
Gene Names: CTSD (CPSD)
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to Gene View: CTSD
Go to UniProtKB:  P07339
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathepsin D heavy chain
B
243Homo sapiensMutation(s): 0 
Gene Names: CTSD (CPSD)
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to Gene View: CTSD
Go to UniProtKB:  P07339
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
2S1
Query on 2S1

Download SDF File 
Download CCD File 
B
2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide
C44 H40 Br Cl2 N3 O8
DQHKQRXAVNDAFY-UWXQCODUSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2S1IC50: 0.7 - 85 nM (100) BINDINGDB
2S1Ki: 0.7 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.207 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.022α = 90.00
b = 77.022β = 90.00
c = 251.586γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references