MolNFT v1 · #66127 · protein
Crystal structure of cathepsin L in complex with AZ12878478
3HHA · Cathepsin L1: “Crystal structure of cathepsin L in complex with AZ12878478”. X-ray diffraction, 1 ligand (NOW), 8 pockets (best druggability 0.79). MolNFT v1 #66127 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HHA
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L1
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- NOW
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cathepsin L1 (EC 3.4.22.15) | protein | 220 | 31% helix, 21% strand | P07711 |
| B | Cathepsin L1 (EC 3.4.22.15) | protein | 216 | 31% helix, 21% strand | P07711 |
| C | Cathepsin L1 (EC 3.4.22.15) | protein | 213 | 31% helix, 21% strand | P07711 |
Ligands and binding sites
- NOW · Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2Z)-2-iminoethyl]-3-methyl-L-phenylalaninamide · ligand · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A
- ACT · Acetate ion · additive · chains A
- PGE · Triethylene glycol · additive · chains B, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.79 | 0.81 | 94 | empty |
| 2 | 208 | 0.60 | 0.81 | 30 | empty |
| 3 | 301 | 0.52 | 0.74 | 51 | PGE, NOW |
| 4 | 89 | 0.47 | 0.81 | 22 | empty |
| 5 | 81 | 0.43 | 0.80 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–D · 516 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 467 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
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 3HHA · PDBe 3HHA · UniProt P07711
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