Research workbench
Coronavirus main proteinase (3CLPRO) structure: basis for design of anti-SARS drugs
Analyse Coronavirus main proteinase (3CLPRO) structure: basis for design of anti-SARS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P9U
- Type
- protein
- Length
- 1,811 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative coronavirus NSP2 (3CL-pro); Phq-vnstlq-chloromethylketone inhibitor
- UniProt
- Q9IW06
- Ligands
- SO4, 0QE
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Putative coronavirus NSP2 (3CL-pro) | protein | 299 | 23% helix, 28% strand | Q9IW06 |
| B, C, F | Putative coronavirus NSP2 (3CL-pro) | protein | 300 | 23% helix, 28% strand | Q9IW06 |
| D | Putative coronavirus NSP2 (3CL-pro) | protein | 301 | 23% helix, 29% strand | Q9IW06 |
| G, H | Phq-vnstlq-chloromethylketone inhibitor | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, F, D, E
- 0QE · Chloromethane · ion · 2 copies · chains B, G, F, H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.78 | 0.80 | 119 | SO4 |
| 2 | 757 | 0.77 | 0.82 | 73 | SO4 |
| 3 | 676 | 0.75 | 0.81 | 61 | SO4 |
| 4 | 514 | 0.70 | 0.80 | 55 | SO4 |
| 5 | 459 | 0.69 | 0.80 | 55 | SO4 |
Interfaces
10 interfaces between chains.
- A–B · 1390 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1390 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1329 Ų buried · 33 hydrogen bonds · protein-protein
- B–G · 533 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 512 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1P9U · Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs · 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 Q9IW06
- Elsewhere: RCSB PDB 1P9U · PDBe 1P9U · UniProt Q9IW06
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