Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39819.77 
• Atom Count: 2748 
• Residue Count: 346 
• Unique protein chains: 2

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

• DOI: 10.2210/pdb4OC6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2014-01-08 Released: 2014-08-13 
• Deposition Author(s): Graedler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Maskos, K., Leuthner, B.

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Experimental Data Snapshot

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

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

• PubMed: 25086681 
• DOI: 10.1016/j.bmcl.2014.07.054
• Primary Citation of Related Structures:  
  4OD9, 4OBZ


• 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 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.

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Organizational Affiliation: 

Merck KGaA, Merck Serono Research, Small Molecule Platform, Frankfurter Str. 250, 64293 Darmstadt, Germany. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cathepsin D light chain	A	103	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Cathepsin D heavy chain	B	243	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
2S1	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
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2S1	IC50: 0.7 - 85 nM (100) BINDINGDB
2S1	Ki: 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 = 77.022	α = 90.00
b = 77.022	β = 90.00
c = 251.586	γ = 120.00

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-08 
• Released Date: 2014-08-13 
• Deposition Author(s): Graedler, U., Czodrowski, P., Tsaklakidis, C., Klein, M., Maskos, K., Leuthner, B.

Revision History 

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