Research workbench
High resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor smdc-256047
Analyse High resolution crystal structure of cruzain bound to the vinyl sulfone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HD3
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cruzipain
- EC
- 3.4.22.51
- UniProt
- P25779
- Ligands
- 25B, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cruzipain (EC 3.4.22.51) | protein | 215 | 26% helix, 23% strand | P25779 |
| B | Cruzipain (EC 3.4.22.51) | protein | 214 | 27% helix, 23% strand | P25779 |
Ligands and binding sites
- 25B · (1R,2R)-2-[(4-chlorophenyl)carbonyl]-N-{(1S)-1-[2-(phenylsulfonyl)ethyl]pentyl}cyclohexanecarboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- EOH · Ethanol · additive · 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 | 467 | 0.67 | 0.79 | 53 | 25B |
| 2 | 62 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3HD3 · High resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P25779 · AlphaFold monomer V2.0 prediction for cruzipain (P25779) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P25779
- Elsewhere: RCSB PDB 3HD3 · PDBe 3HD3 · UniProt P25779
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