MolNFT v1 · #179202 · protein
Crystal structure of SARS-cov-2 main protease (3CLPRO/MPRO) in complex with covalent inhibitor narlaprevir
7JYC · 3C-like proteinase: “Crystal structure of SARS-cov-2 main protease (3CLPRO/MPRO) in complex with covalent inhibitor narlaprevir”. X-ray diffraction, 2 ligands (NNA, NA), 3 pockets (best druggability 0.53). MolNFT v1 #179202 on…
- PDB
- 7JYC
- Type
- protein
- Length
- 306 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
- NNA, NA
- Pockets
- 3 · best druggability 0.53
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 | 306 | 25% helix, 28% strand | P0DTD1 |
Ligands and binding sites
- NNA · (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl) methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · 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 | 220 | 0.53 | 0.77 | 30 | NNA |
| 2 | 174 | 0.51 | 0.78 | 30 | DMS |
| 3 | 52 | 0.29 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7JYC · Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent… · 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 7JYC · PDBe 7JYC · UniProt P0DTD1
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