MolNFT v1 · #14694 · protein
Design of non-covalent inhibitors of human cathepsin L. from the 96- residue proregion to optimized tripeptides
1MHW: “Design of non-covalent inhibitors of human cathepsin L. from the 96- residue proregion to optimized…”. X-ray diffraction, 2 ligands (BP4, PEA), 1 pocket (best druggability 0.59). MolNFT v1 #14694 on GenesisL1: 3D structure, binding…
- PDB
- 1MHW
- Type
- protein
- Length
- 440 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L; 4-biphenylacetyl-cys-(D)ARG-tyr-N-(2-phenylethyl) amide
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- BP4, PEA
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin L (EC 3.4.22.15) | protein | 174 | 34% helix, 17% strand | P07711 |
| C, D | Cathepsin L (EC 3.4.22.15) | protein | 41 | 7% helix, 39% strand | P07711 |
| E, F | 4-biphenylacetyl-cys-(D)ARG-tyr-N-(2-phenylethyl) amide | protein | 2 | 0% helix, 0% strand | — |
| G, H | 4-biphenylacetyl-cys-(D)ARG-tyr-N-(2-phenylethyl) amide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- BP4 · biphenyl-4-ylacetic acid · ligand · 4 copies · chains A, B, D, E, C, F, G, H
- PEA · 2-phenylethylamine · ligand · 2 copies · chains A, G, B, H
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 | 381 | 0.59 | 0.76 | 33 | BP4 |
Interfaces
17 interfaces between chains.
- B–D · 2523 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 2416 Ų buried · 47 hydrogen bonds · protein-protein
- B–H · 359 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 357 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 265 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 covalent, 4 d-amino, 2 modified (disulfide, covalent ligand, D-amino acid, oxidation).
Compared structures
- 1MHW · Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to… · the same entry in another collection · chain H against H, 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 1MHW · PDBe 1MHW · UniProt P07711
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