MolNFT v1 · #170281 · protein
Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-cov-2 (2019-ncov) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3- YL)BUTAN-2-YL)AMINO)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2- dihydropyridin-3-YL)CARBAMATE (alpha-ketoamide 13B)
6Y2F · 3C-like proteinase: “Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-cov-2 (2019-ncov)…”. X-ray diffraction, 1 ligand (O6K), 2 pockets (best druggability 0.50). MolNFT v1 #170281 on…
- PDB
- 6Y2F
- Type
- protein
- Length
- 303 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
- O6K
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- O6K · ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate · 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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.50 | 0.76 | 28 | DMS, O6K |
| 2 | 139 | 0.41 | 0.74 | 25 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6Y2F · Crystal structure (monoclinic form) of the complex resulting from the reaction between… · 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 6Y2F · PDBe 6Y2F · UniProt P0DTD1
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