MolNFT v1 · #65824 · protein
A combined crystallographic and molecular dynamics study of cathepsin- L retro-binding INHIBITORS(COMPOUND 9)
3H8B · Cathepsin L1: “A combined crystallographic and molecular dynamics study of cathepsin- L retro-binding INHIBITORS(COMPOUND 9)”. X-ray diffraction, 1 ligand (NSY), 16 pockets (best druggability 0.78). MolNFT v1 #65824 on GenesisL1: 3D…
- PDB
- 3H8B
- 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
- NSY
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cathepsin L1 (EC 3.4.22.15) | protein | 215 | 28% helix, 22% strand | P07711 |
Ligands and binding sites
- NSY · N~2~,N~6~-bis(biphenyl-4-ylacetyl)-L-lysyl-D-arginyl-N-(2-phenylethyl)-L-phenylalaninamide · ligand · 6 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.78 | 0.85 | 65 | NSY |
| 2 | 837 | 0.76 | 0.80 | 89 | NSY |
| 3 | 191 | 0.58 | 0.81 | 46 | empty |
| 4 | 240 | 0.57 | 0.79 | 48 | empty |
| 5 | 195 | 0.49 | 0.76 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–E · 642 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 641 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 558 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 554 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3H8B · A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding… · the same entry in another collection · chain F against F, 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 3H8B · PDBe 3H8B · UniProt P07711
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