MolNFT v1 · #180315 · protein
SARS-cov-2 main protease immature form - fmax library E09 fragment
7KVR · 3C-like proteinase: “SARS-cov-2 main protease immature form - fmax library E09 fragment”. X-ray diffraction, 1 ligand (X4V), 5 pockets (best druggability 0.79). MolNFT v1 #180315 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7KVR
- Type
- protein
- Length
- 600 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
- X4V
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 25% helix, 30% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- X4V · N~4~,N~4~-dimethylpyridine-2,4-diamine · ligand · chains B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.79 | 0.81 | 78 | DMS, PEG |
| 2 | 857 | 0.72 | 0.77 | 113 | DMS |
| 3 | 199 | 0.49 | 0.76 | 25 | empty |
| 4 | 167 | 0.49 | 0.77 | 28 | empty |
| 5 | 165 | 0.48 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7KVR · SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment · 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 7KVR · PDBe 7KVR · UniProt P0DTD1
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