MolNFT v1 · #47126 · protein
Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus
2OP9 · Replicase polyprotein 1AB (PP1AB, ORF1AB) 3C-like…: “Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the…”. X-ray diffraction, 1 ligand (WR1), 6 pockets (best druggability…
- PDB
- 2OP9
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB (PP1AB, ORF1AB) 3C-like proteinase (3CL-pro, 3CLP)
- EC
- 3.4.22.-
- UniProt
- P59641
- Ligands
- WR1
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB (PP1AB, ORF1AB) 3C-like proteinase (3CL-pro, 3CLP) (EC 3.4.22.-) | protein | 302 | 26% helix, 30% strand | P59641 |
| B | Replicase polyprotein 1AB (PP1AB, ORF1AB) 3C-like proteinase (3CL-pro, 3CLP) (EC 3.4.22.-) | protein | 299 | 25% helix, 29% strand | P59641 |
Ligands and binding sites
- WR1 · Nalpha-[(benzyloxy)carbonyl]-N-[(1R)-4-hydroxy-1-methyl-2-oxobutyl]-L-phenylalaninamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.76 | 0.79 | 72 | empty |
| 2 | 646 | 0.66 | 0.76 | 85 | empty |
| 3 | 210 | 0.50 | 0.76 | 29 | WR1 |
| 4 | 178 | 0.46 | 0.75 | 28 | WR1 |
| 5 | 155 | 0.43 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1276 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2OP9 · Substrate Specificity Profiling and Identification of a New Class of Inhibitor for the… · 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 2OP9 · PDBe 2OP9 · UniProt P59641
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