Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 39.77 kDa 
• Atom Count: 2758 
• Residue Count: 341 
• 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
• Mutation(s): No 


• 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 
• R-Value Observed: 0.211 

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:  
  4OBZ, 4OC6, 4OD9


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P07339  Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS:  P07339 GTEx:  ENSG00000117984

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P07339  Go to UniProtKB:  P07339
NIH Common Fund Data Resources
PHAROS:  P07339 GTEx:  ENSG00000117984

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2S1	IC50:  85   nM  BindingDB
2S1	IC50:  0.699999988079071   nM  BindingDB
2S1	Ki:  0.699999988079071   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.282 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.022	α = 90
b = 77.022	β = 90
c = 251.586	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

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
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary