MolNFT v1 · #65822 · protein
A combined crystallographic and molecular dynamics study of cathepsin- L retro-binding INHIBITORS(COMPOUND 4)
3H89 · Cathepsin L1: “A combined crystallographic and molecular dynamics study of cathepsin- L retro-binding INHIBITORS(COMPOUND 4)”. X-ray diffraction, 1 ligand (NSX), 7 pockets (best druggability 0.42). MolNFT v1 #65822 on GenesisL1: 3D…
- PDB
- 3H89
- Type
- protein
- Length
- 1,290 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L1
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- NSX
- Pockets
- 7 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cathepsin L1 (EC 3.4.22.15) | protein | 215 | 29% helix, 21% strand | P07711 |
Ligands and binding sites
- NSX · N~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-tyrosinamide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.42 | 0.72 | 24 | empty |
| 2 | 59 | 0.34 | 0.77 | 14 | empty |
| 3 | 65 | 0.33 | 0.76 | 17 | empty |
| 4 | 77 | 0.33 | 0.75 | 18 | empty |
| 5 | 74 | 0.32 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3H89 · A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P07711
- Elsewhere: RCSB PDB 3H89 · PDBe 3H89 · UniProt P07711
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