MolNFT v1 · #175849 · protein
Crystal structure of SARS-cov-2 main protease in complex with mi-23
7D3I · 3C-like proteinase: “Crystal structure of SARS-cov-2 main protease in complex with mi-23”. X-ray diffraction, 1 ligand (GQU), 2 pockets (best druggability 0.48). MolNFT v1 #175849 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D3I
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- GQU
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- GQU · (3~{S},3~{A}~{S},6~{A}~{R})-2-[3-[3,5-bis(fluoranyl) phenyl]propanoyl]-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{A},4,5,6,6~{A}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.48 | 0.75 | 25 | GQU |
| 2 | 91 | 0.38 | 0.76 | 26 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7D3I · Crystal structure of SARS-CoV-2 main protease in complex with MI-23 · 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 P0DTC1
- Elsewhere: RCSB PDB 7D3I · PDBe 7D3I · UniProt P0DTC1
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