MolNFT v1 · #180483 · protein
Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 26
7L14 · 3C-like proteinase: “Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 26”. X-ray diffraction, 1 ligand (XFD), 6 pockets (best druggability 0.77). MolNFT v1 #180483 on GenesisL1: 3D structure…
- PDB
- 7L14
- Type
- protein
- Length
- 611 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
- XFD
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% 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 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- XFD · 2-{3-[3-chloro-5-(cyclopropylmethoxy)phenyl]-2-oxo[2H-[1,3'-bipyridine]]-5-yl}benzonitrile · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.77 | 0.80 | 81 | empty |
| 2 | 372 | 0.55 | 0.74 | 56 | empty |
| 3 | 258 | 0.53 | 0.75 | 34 | empty |
| 4 | 237 | 0.51 | 0.76 | 37 | XFD |
| 5 | 182 | 0.46 | 0.75 | 29 | XFD |
Interfaces
1 interface between chains.
- A–B · 1494 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7L14 · Crystal structure of the SARS-cov-2(2019-ncov) main protease in complex with compound 26 · 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 7L14 · PDBe 7L14 · UniProt P0DTD1
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