MolNFT v1 · #109251 · protein
Crystal structure of human adenovirus 8 protease with an irreversible vinyl sulfone inhibitor
4WX6: “Crystal structure of human adenovirus 8 protease with an irreversible vinyl sulfone inhibitor”. X-ray diffraction, 1 ligand (3VK), 3 pockets (best druggability 0.64). MolNFT v1 #109251 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4WX6
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease; Pvi
- EC
- 3.4.22.39
- UniProt
- B9A5C1, B9A5F5
- Ligands
- 3VK
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protease (EC 3.4.22.39) | protein | 204 | 41% helix, 17% strand | B9A5C1 |
| B, D | Pvi | protein | 11 | 0% helix, 64% strand | B9A5F5 |
Ligands and binding sites
- 3VK · N-[(2S)-2-(3,5-dichlorophenyl)-2-(ethylamino)acetyl]-3-methyl-L-valyl-N-[3-(methylsulfonyl)propyl]glycinamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.64 | 0.77 | 48 | empty |
| 2 | 136 | 0.43 | 0.76 | 34 | 3VK |
| 3 | 112 | 0.41 | 0.76 | 26 | 3VK |
Interfaces
3 interfaces between chains.
- A–B · 926 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 905 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4WX6 · Crystal structure of human adenovirus 8 protease with an irreversible vinyl sulfone… · 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 B9A5C1
- Every structure of UniProt B9A5F5
- Elsewhere: RCSB PDB 4WX6 · PDBe 4WX6 · UniProt B9A5C1 · UniProt B9A5F5
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