MolNFT v1 · #38706 · protein
An episulfide cation (thiiranium ring) trapped in the active site of hav 3C proteinase inactivated by peptide-based ketone inhibitors
2H6M · Picornain 3C: “An episulfide cation (thiiranium ring) trapped in the active site of hav 3C proteinase inactivated by…”. X-ray diffraction, 3 ligands (ACE, BBL, CF0), 2 pockets (best druggability 0.47). MolNFT v1 #38706 on GenesisL1…
- PDB
- 2H6M
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Picornain 3C; N-acetyl-leucyl-alanyl-alanyl-(N,N-dimethyl)-glutamine-(1…
- EC
- 3.4.22.28
- UniProt
- P06441
- Ligands
- ACE, BBL, CF0
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Picornain 3C (EC 3.4.22.28) | protein | 212 | 18% helix, 49% strand | P06441 |
| I | N-acetyl-leucyl-alanyl-alanyl-(N,N-dimethyl)-glutamine-(1, 4-dioxo-3,4-dihydro-1H-phthalazin-2-YL)METHYLKETONE inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, I
- BBL · N-[(benzyloxy)carbonyl]-L-alanine · ligand · chains A
- CF0 · Fluoromethane · ion · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.47 | 0.78 | 23 | empty |
| 2 | 57 | 0.31 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–I · 438 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2H6M · An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase… · the same entry in another collection · chain I against I, 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 P06441
- Elsewhere: RCSB PDB 2H6M · PDBe 2H6M · UniProt P06441
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