Research workbench
The newly emerged SARS-like coronavirus hcov-emc also has an "achilles' heel": current effective inhibitor targeting a 3C-like protease
Analyse The newly emerged SARS-like coronavirus hcov-emc also has an "achilles' heel"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D3C
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~…
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- A0A0D3MU45
- Ligands
- 02J, PJE, 010
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 299 | 25% helix, 30% strand | A0A0D3MU45 |
| A | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 303 | 24% helix, 29% strand | A0A0D3MU45 |
| C, E | N-[(5-methylisoxazol-3-YL)CARBONYL]ALANYL-L-valyl-N~1~- ((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3- YL]METHYL}BUT-2-enyl)-L-leucinamide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 2 copies · chains A, C, B, E
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 2 copies · chains A, C, B, E
- 010 · phenylmethanol · ligand · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.76 | 0.78 | 62 | empty |
| 2 | 398 | 0.58 | 0.75 | 48 | empty |
| 3 | 380 | 0.58 | 0.75 | 54 | empty |
| 4 | 90 | 0.41 | 0.78 | 22 | PJE, 010 |
| 5 | 89 | 0.40 | 0.77 | 23 | PJE, 010 |
Interfaces
3 interfaces between chains.
- B–A · 1212 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 321 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7D3C · The newly emerged SARS-like coronavirus HCoV-EMC also has an "Achilles' heel": current… · the same entry in another collection · chain B against B, 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 A0A0D3MU45
- Elsewhere: RCSB PDB 7D3C · PDBe 7D3C · UniProt A0A0D3MU45
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