MolNFT v1 · #188200 · protein
Structure of SARS-cov-2 main protease in complex with GC376
7TGR · 3C-like proteinase: “Structure of SARS-cov-2 main protease in complex with GC376”. X-ray diffraction, 5 ligands (K36, B1S, K), 2 pockets (best druggability 0.53). MolNFT v1 #188200 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TGR
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- K36, B1S, K, NA, CL
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- K36 · (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
- B1S · (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
- K · Potassium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.53 | 0.78 | 25 | K36, B1S |
| 2 | 225 | 0.49 | 0.75 | 32 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7TGR · Structure of SARS-CoV-2 main protease in complex with GC376 · 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 7TGR · PDBe 7TGR · UniProt P0DTD1
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