MolNFT v1 · #78262 · protein
Structure of cathepsin B1 from schistosoma mansoni in complex with K11777 inhibitor
3S3R · Cathepsin B-like peptidase (C01 family): “Structure of cathepsin B1 from schistosoma mansoni in complex with K11777 inhibitor”. X-ray diffraction, 1 ligand (0IW), 7 pockets (best druggability 0.76). MolNFT v1 #78262 on GenesisL1: 3D…
- PDB
- 3S3R
- Type
- protein
- Length
- 756 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like peptidase (C01 family)
- EC
- 3.4.22.1
- UniProt
- Q8MNY2
- Ligands
- 0IW
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 254 | 24% helix, 23% strand | Q8MNY2 |
| B | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 249 | 23% helix, 25% strand | Q8MNY2 |
| C | Cathepsin B-like peptidase (C01 family) (EC 3.4.22.1) | protein | 253 | 24% helix, 25% strand | Q8MNY2 |
Ligands and binding sites
- 0IW · Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.76 | 0.78 | 111 | 0IW |
| 2 | 1100 | 0.75 | 0.78 | 98 | 0IW |
| 3 | 199 | 0.51 | 0.77 | 25 | 0IW |
| 4 | 64 | 0.43 | 0.82 | 20 | empty |
| 5 | 55 | 0.31 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–C · 392 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 370 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 3S3R · Structure of cathepsin B1 from Schistosoma mansoni in complex with K11777 inhibitor · the same entry in another collection · chain B against B, 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 Q8MNY2
- Elsewhere: RCSB PDB 3S3R · PDBe 3S3R · UniProt Q8MNY2
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