4OD9

Structure of Cathepsin D with inhibitor N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin D light chain
A, C
103Homo sapiensMutation(s): 0 
Gene Names: CPSDCTSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS  P07339
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathepsin D heavy chain
B, D
243Homo sapiensMutation(s): 0 
Gene Names: CPSDCTSD
EC: 3.4.23.5
Find proteins for P07339 (Homo sapiens)
Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS  P07339
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2RZ
Query on 2RZ

Download CCD File 
A, D
N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide
C29 H34 N4 O6
IZIUZEPBXLRZLW-JOCHJYFZSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
B, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2RZIC50:  58   nM  BindingDB
2RZIC50:  330   nM  BindingDB
2RZIC50:  58   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.48α = 90
b = 73.1β = 90
c = 234.19γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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