MolNFT v1 · #170762 · protein
Structure of cathepsin B1 from schistosoma mansoni (SMCB1) in complex with an azanitrile inhibitor
6YI7 · Cathepsin B-like peptidase (C01 family): “Structure of cathepsin B1 from schistosoma mansoni (SMCB1) in complex with an azanitrile inhibitor”. X-ray diffraction, 1 ligand (ORW), 2 pockets (best druggability 0.51). MolNFT v1 #170762…
- PDB
- 6YI7
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like peptidase (C01 family)
- UniProt
- Q8MNY2
- Ligands
- ORW
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B-like peptidase (C01 family) | protein | 254 | 28% helix, 23% strand | Q8MNY2 |
Ligands and binding sites
- ORW · 1-[(2~{S})-1-[[iminomethyl(methyl)amino]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-3-(phenylmethyl)urea · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.51 | 0.76 | 33 | ORW |
| 2 | 68 | 0.34 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6YI7 · Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with an azanitrile… · the same entry in another collection · 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 Q8MNY2
- Elsewhere: RCSB PDB 6YI7 · PDBe 6YI7 · UniProt Q8MNY2
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