MolNFT v1 · #171164 · protein
Eed in complex with a cyano-benzofuran
6YVI · Polycomb protein eed: “Eed in complex with a cyano-benzofuran”. X-ray diffraction, 3 ligands (L9W, PV5, CA), 7 pockets (best druggability 0.78). MolNFT v1 #171164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YVI
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed
- UniProt
- O75530
- Ligands
- L9W, PV5, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 350 | 4% helix, 47% strand | O75530 |
| B | Polycomb protein eed | protein | 344 | 3% helix, 50% strand | O75530 |
Ligands and binding sites
- L9W · N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine · ligand · chains A
- PV5 · 5-fluoranyl-4-[[[8-(2-methylpyridin-3-yl)-[1,2, 4]triazolo[4,3-c]pyrimidin-5-yl]amino]methyl]-2,3-dihydro-1-benzofuran-7-carbonitrile · ligand · chains B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.78 | 0.86 | 42 | empty |
| 2 | 466 | 0.77 | 0.85 | 41 | empty |
| 3 | 76 | 0.55 | 0.87 | 12 | PV5 |
| 4 | 60 | 0.55 | 0.88 | 10 | L9W |
| 5 | 100 | 0.38 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 225 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 O75530
- Elsewhere: RCSB PDB 6YVI · PDBe 6YVI · UniProt O75530
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