MolNFT v1 · #179133 · protein
Crystal structure of SARS-cov-2 3CL protease in complex with compound 4 in space group P1
7JW8 · 3C-like proteinase: “Crystal structure of SARS-cov-2 3CL protease in complex with compound 4 in space group P1”. X-ray diffraction, 1 ligand (TG3), 15 pockets (best druggability 0.77). MolNFT v1 #179133 on GenesisL1: 3D structure…
- PDB
- 7JW8
- Type
- protein
- Length
- 1,222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- TG3
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 29% strand | P0DTD1 |
| B, C | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- TG3 · Ethyl (4R)-4-[[(2S)-4-methyl-2-[[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-2-(phenylmethoxycarbonylamino) butanoyl]amino]pentanoyl]amino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate · ligand · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.77 | 0.80 | 84 | empty |
| 2 | 1047 | 0.77 | 0.79 | 90 | empty |
| 3 | 549 | 0.63 | 0.75 | 80 | empty |
| 4 | 261 | 0.57 | 0.78 | 37 | TG3 |
| 5 | 233 | 0.55 | 0.78 | 30 | TG3 |
Interfaces
3 interfaces between chains.
- A–B · 1468 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1428 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7JW8 · Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4 in space group P1 · 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 P0DTD1
- Elsewhere: RCSB PDB 7JW8 · PDBe 7JW8 · UniProt P0DTD1
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