MolNFT v1 · #3442 · protein
Crystal structure of cathepsin B inhibited with CA030 at 2.1 ångströms resolution: a basis for the design of specific epoxysuccinyl inhibitors
1CSB · Cathepsin B light chain: “Crystal structure of cathepsin B inhibited with CA030 at 2.1 ångströms resolution: a basis for the design of…”. X-ray diffraction, 1 ligand (EP0), 5 pockets (best druggability 0.50). MolNFT v1 #3442 on…
- PDB
- 1CSB
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B light chain; Cathepsin B heavy chain
- EC
- 3.4.22.1
- UniProt
- P07858
- Ligands
- EP0
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cathepsin B light chain (EC 3.4.22.1) | protein | 47 | 49% helix, 9% strand | P07858 |
| B, E | Cathepsin B heavy chain (EC 3.4.22.1) | protein | 205 | 20% helix, 30% strand | P07858 |
Ligands and binding sites
- EP0 · N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline · ligand · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.50 | 0.77 | 30 | EP0 |
| 2 | 219 | 0.50 | 0.75 | 34 | EP0 |
| 3 | 126 | 0.36 | 0.73 | 23 | empty |
| 4 | 85 | 0.33 | 0.74 | 17 | empty |
| 5 | 58 | 0.25 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2351 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2304 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1CSB · Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A… · the same entry in another collection · chain E against E, TM-score 1.00
- P07858 · AlphaFold monomer V2.0 prediction for cathepsin B (P07858) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P07858
- Elsewhere: RCSB PDB 1CSB · PDBe 1CSB · UniProt P07858
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