› 4oc6

X-ray diffraction
2.64Å resolution

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

Released:
DOI: 10.2210/pdb4oc6/pdb
PDB entry 4oc6 coloured by chain, front view.
PDB entry 4oc6 coloured by chain, side view.
PDB entry 4oc6 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 Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand 2S1 1 x 2S1
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P6122
Unit cell:
a: 77.022Å b: 77.022Å c: 251.586Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.207 0.282
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

Bridging the Gap in Malaria Parasite Resistance, Current Interventions, and the Way Forward from in Silico Perspective: A Review.
Kumi et al. (2022)
5 other articles

1 mention without citation

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