MolNFT v1 · #102106 · protein
Structure of cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N- (4-METHYLBENZYL)CARBAMIMIDOYL]ACETAMIDE
4OBZ · Cathepsin D light chain: “Structure of cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N- (4-METHYLBENZYL)CARBAMIMIDOYL]ACETAMIDE”. X-ray diffraction, 2 ligands (2S4, NAG), 4 pockets (best druggability 0.70). MolNFT v1 #102106…
- PDB
- 4OBZ
- Type
- protein
- Length
- 677 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin D light chain; Cathepsin D heavy chain
- EC
- 3.4.23.5
- UniProt
- P07339
- Ligands
- 2S4, NAG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin D light chain (EC 3.4.23.5) | protein | 97 | 7% helix, 55% strand | P07339 |
| B | Cathepsin D heavy chain (EC 3.4.23.5) | protein | 240 | 16% helix, 45% strand | P07339 |
| C | Cathepsin D light chain (EC 3.4.23.5) | protein | 103 | 7% helix, 51% strand | P07339 |
| D | Cathepsin D heavy chain (EC 3.4.23.5) | protein | 237 | 16% helix, 43% strand | P07339 |
Ligands and binding sites
- 2S4 · 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.70 | 0.77 | 69 | empty |
| 2 | 772 | 0.70 | 0.76 | 66 | 2S4 |
| 3 | 92 | 0.33 | 0.73 | 20 | empty |
| 4 | 80 | 0.30 | 0.73 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3205 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 3190 Ų buried · 82 hydrogen bonds · protein-protein
- A–D · 101 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4OBZ · Structure of Cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carba… · the same entry in another collection · chain D against D, TM-score 1.00
- P07339 · AlphaFold monomer V2.0 prediction for cathepsin D (P07339) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07339
- Elsewhere: RCSB PDB 4OBZ · PDBe 4OBZ · UniProt P07339
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