MolNFT v1 · #181611 · protein
Structure of SARS-cov-2 3CL protease in complex with inhibitor 13C
7M00 · 3C-like proteinase: “Structure of SARS-cov-2 3CL protease in complex with inhibitor 13C”. X-ray diffraction, 2 ligands (YKA, YKD), 6 pockets (best druggability 0.75). MolNFT v1 #181611 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7M00
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- YKA, YKD
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 295 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 297 | 26% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- YKA · (1R,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl) propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- YKD · (1S,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl) propane-1-sulfonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.75 | 0.78 | 74 | empty |
| 2 | 198 | 0.53 | 0.78 | 25 | YKA, YKD |
| 3 | 184 | 0.52 | 0.78 | 24 | YKA, YKD |
| 4 | 82 | 0.48 | 0.82 | 20 | empty |
| 5 | 100 | 0.44 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7M00 · Structure of SARS-CoV-2 3CL protease in complex with inhibitor 13c · 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 7M00 · PDBe 7M00 · UniProt P0DTD1
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