ISDA

Deposition Date 2014-01-08

Release Date 2014-08-13

Last Version Date 2024-11-27

Entry Detail

PDB ID:

4OC6

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.64 Å

R-Value Free:

0.28

R-Value Work:

0.20

R-Value Observed:

0.21

Space Group:

P 61 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cathepsin D light chain
Gene (Uniprot):CTSD
Chain IDs:A
Chain Length:103
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P07339 Pfam ID:PF00026 EC:3.4.23.5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cathepsin D heavy chain
Gene (Uniprot):CTSD
Chain IDs:B
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P07339 Pfam ID:PF00026 EC:3.4.23.5

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ASN	A	ASN	GLYCOSYLATION SITE

Ligand Molecules

2S1

GOL

NAG

Primary Citation

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.Show

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

PMID: 25086681 DOI: 10.1016/j.bmcl.2014.07.054

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures