MolNFT v1 · #31188 · protein
Crystal structure of SARS_COV mpro in complex with an inhibitor N3
2AMQ · 3C-like proteinase: “Crystal structure of SARS_COV mpro in complex with an inhibitor N3”. X-ray diffraction, 3 ligands (02J, PJE, 010), 6 pockets (best druggability 0.75). MolNFT v1 #31188 on GenesisL1: 3D structure, binding sites…
- PDB
- 2AMQ
- Type
- protein
- Length
- 611 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
- 3.4.22.-
- UniProt
- P59641
- Ligands
- 02J, PJE, 010
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 303 | 25% helix, 29% strand | P59641 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 302 | 25% helix, 31% strand | P59641 |
| C, D | 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, D
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 2 copies · chains A, C, B, D
- 010 · phenylmethanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.75 | 0.78 | 74 | empty |
| 2 | 370 | 0.56 | 0.75 | 58 | empty |
| 3 | 205 | 0.54 | 0.78 | 33 | empty |
| 4 | 104 | 0.48 | 0.80 | 22 | PJE, 010 |
| 5 | 85 | 0.41 | 0.78 | 19 | PJE, 010 |
Interfaces
3 interfaces between chains.
- A–B · 1273 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 343 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 2AMQ · Crystal Structure Of SARS_CoV Mpro in Complex with an Inhibitor N3 · 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 P59641
- Elsewhere: RCSB PDB 2AMQ · PDBe 2AMQ · UniProt P59641
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