MolNFT v1 · #175570 · protein
Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with Z-vad-fmk
7CUT · 3C protein: “Crystal structure of the SARS-cov-2 (COVID-19) main protease in complex with Z-vad-fmk”. X-ray diffraction, 2 ligands (PHQ, CF0), 1 pocket (best druggability 0.39). MolNFT v1 #175570 on GenesisL1: 3D structure, binding…
- PDB
- 7CUT
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C protein; Z-VAD(OME)-fmk
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- PHQ, CF0
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C protein (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTD1 |
| B | Z-VAD(OME)-fmk | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A, B
- CF0 · Fluoromethane · ion · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.39 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 299 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 7CUT · Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with Z-VAD-FMK · 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 7CUT · PDBe 7CUT · UniProt P0DTD1
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