MolNFT v1 · #179464 · protein
SARS-cov-2 main protease co-crystal structure with telaprevir determined from crystals grown with 40 nl acoustically ejected mpro droplets at 1.48 a resolution (cryo-protected)
7K6D · 3C-like proteinase: “SARS-cov-2 main protease co-crystal structure with telaprevir determined from crystals grown with 40 nl…”. X-ray diffraction, 1 ligand (SV6), 3 pockets (best druggability 0.55). MolNFT v1 #179464 on GenesisL1…
- PDB
- 7K6D
- Type
- protein
- Length
- 305 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
- SV6
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- SV6 · (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.55 | 0.87 | 16 | DMS |
| 2 | 217 | 0.52 | 0.76 | 29 | SV6 |
| 3 | 170 | 0.44 | 0.74 | 30 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7K6D · SARS-CoV-2 Main Protease Co-Crystal Structure with Telaprevir Determined from Crystals… · 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 7K6D · PDBe 7K6D · UniProt P0DTD1
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