MolNFT v1 · #184816 · protein
Eed in complex with compound 4
7P3J · Polycomb protein eed: “Eed in complex with compound 4”. X-ray diffraction, 3 ligands (L9W, 54N, MG), 7 pockets (best druggability 0.76). MolNFT v1 #184816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7P3J
- 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, 54N, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 350 | 3% helix, 47% strand | O75530 |
| B | Polycomb protein eed | protein | 344 | 3% helix, 49% 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
- 54N · 8-[6-[(dimethylamino)methyl]-2-methyl-pyridin-3-yl]-5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl) methylamino]-2H-pyrido[3,4-d]pyridazin-1-one · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · 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 | 422 | 0.76 | 0.86 | 37 | empty |
| 2 | 456 | 0.76 | 0.85 | 38 | empty |
| 3 | 61 | 0.55 | 0.88 | 11 | L9W |
| 4 | 84 | 0.54 | 0.85 | 13 | 54N |
| 5 | 100 | 0.36 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 229 Ų buried · 2 hydrogen bonds · 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 7P3J · PDBe 7P3J · UniProt O75530
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