MolNFT v1 · #174745 · protein
Crystal structure of SARS-cov-2 HR1 motif in complex with pan-covs inhibitor EK1
7C53 · Spike protein S2',PAN-covs inhibitor EK1: “Crystal structure of SARS-cov-2 HR1 motif in complex with pan-covs inhibitor EK1”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.78). MolNFT v1 #174745 on GenesisL1: 3D…
- PDB
- 7C53
- Type
- protein
- Length
- 551 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S2',PAN-covs inhibitor EK1
- UniProt
- P0DTC2
- Ligands
- CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S2',PAN-covs inhibitor EK1 | protein | 93 | 78% helix, 0% strand | P0DTC2 |
| B | Spike protein S2',PAN-covs inhibitor EK1 | protein | 93 | 77% helix, 0% strand | P0DTC2 |
| C | Spike protein S2',PAN-covs inhibitor EK1 | protein | 91 | 77% helix, 0% strand | P0DTC2 |
| D | Spike protein S2',PAN-covs inhibitor EK1 | protein | 89 | 78% helix, 0% strand | P0DTC2 |
| E | Spike protein S2',PAN-covs inhibitor EK1 | protein | 93 | 77% helix, 0% strand | P0DTC2 |
| F | Spike protein S2',PAN-covs inhibitor EK1 | protein | 92 | 77% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.78 | 0.83 | 73 | CA |
| 2 | 65 | 0.76 | 1.00 | 15 | empty |
| 3 | 65 | 0.75 | 0.99 | 15 | empty |
| 4 | 52 | 0.72 | 0.99 | 13 | empty |
| 5 | 54 | 0.30 | 0.76 | 12 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1646 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1605 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1596 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1576 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1560 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7C53 · Crystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoVs inhibitor EK1 · 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 P0DTC2
- Elsewhere: RCSB PDB 7C53 · PDBe 7C53 · UniProt P0DTC2
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