MolNFT v1 · #172814 · protein
SARS-cov-2 main protease in a covalent complex with a pyridine derivative of abt-957, compound 1
7AEH · 3C-like proteinase NSP5: “SARS-cov-2 main protease in a covalent complex with a pyridine derivative of abt-957, compound 1”. X-ray diffraction, 1 ligand (R8H), 4 pockets (best druggability 0.52). MolNFT v1 #172814 on GenesisL1: 3D…
- PDB
- 7AEH
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- R8H
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- R8H · (2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino) butan-2-yl]-1-(phenylmethyl)pyrrolidine-2-carboxamide · ligand · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.52 | 0.87 | 16 | DMS |
| 2 | 207 | 0.50 | 0.76 | 26 | R8H |
| 3 | 62 | 0.34 | 0.77 | 18 | empty |
| 4 | 95 | 0.34 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7AEH · SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957… · 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 7AEH · PDBe 7AEH · UniProt P0DTD1
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