Research workbench
Crystal structure of ns-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft
Analyse Crystal structure of ns-134 in complex with bovine cathepsin B: a two headed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SP4
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B
- EC
- 3.4.22.1
- UniProt
- P07688
- Ligands
- EP2
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B (EC 3.4.22.1) | protein | 48 | 50% helix, 8% strand | P07688 |
| B | Cathepsin B (EC 3.4.22.1) | protein | 205 | 20% helix, 30% strand | P07688 |
Ligands and binding sites
- EP2 · methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.52 | 0.78 | 28 | EP2 |
Interfaces
1 interface between chains.
- A–B · 2440 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1SP4 · Crystal structure of NS-134 in complex with bovine cathepsin B: a two headed… · the same entry in another collection · chain A against A, TM-score 1.00
- P07688 · AlphaFold monomer V2.0 prediction for cathepsin B (P07688) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P07688
- Elsewhere: RCSB PDB 1SP4 · PDBe 1SP4 · UniProt P07688
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