Research workbench
Structure of cathepsin B1 from schistosoma mansoni (SMCB1) in complex with an azanitrile inhibitor
Analyse Structure of cathepsin B1 from schistosoma mansoni (SMCB1) in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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