› 4obz

X-ray diffraction
2.9Å resolution

Structure of Cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide

Released:
DOI: 10.2210/pdb4obz/pdb
PDB entry 4obz coloured by chain, front view.
PDB entry 4obz coloured by chain, side view.
PDB entry 4obz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based optimization of non-peptidic Cathepsin D inhibitors.
Grädler U, Czodrowski P, Tsaklakidis C, Klein M, Werkmann D, Lindemann S, Maskos K, Leuthner B
Bioorg Med Chem Lett 24 4141-50 (2014)
PMID: 25086681

Function and Biology Details

Reaction catalysed: 
Specificity similar to, but narrower than, that of pepsin A. Does not cleave the 4-Gln-|-His-5 bond in B chain of insulin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139523 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Cathepsin D light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 103 amino acids
Theoretical weight: 11.27 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P07339 (Residues: 60-162; Coverage: 26%)
Gene names: CPSD, CTSD
Structure domains: Acid Proteases
Cathepsin D heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 243 amino acids
Theoretical weight: 26.54 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P07339 (Residues: 170-412; Coverage: 62%)
Gene names: CPSD, CTSD
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand 2S4 1 x 2S4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 230.34Å b: 42.454Å c: 73.216Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.232
Expression system: Spodoptera frugiperda

Quick links

Citations

2 citation in other articles

Cathepsin D inhibitors as potential therapeutics for breast cancer treatment: Molecular docking and bioevaluation against triple-negative and triple-positive breast cancers.
Anantaraju et al. (2016)
1 more

6 mentions without citation

Cathepsin D-Managing the Delicate Balance.
Mijanovic et al. (2021)
5 more