MolNFT v1 · #135655 · protein
Crystal structure of eed in complex with 6-(2-fluoro-5-methoxybenzyl)- 1-isopropyl-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-amine 6-(2- fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-TETRAHYDROIMIDAZO[1,5- A]PYRIDIN-3-amine
5U5H · Polycomb protein eed: “Crystal structure of eed in complex with 6-(2-fluoro-5-methoxybenzyl)…”. X-ray diffraction, 1 ligand (7VV), 3 pockets (best druggability 0.77). MolNFT v1 #135655 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U5H
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed
- UniProt
- O75530
- Ligands
- 7VV
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 355 | 3% helix, 47% strand | O75530 |
Ligands and binding sites
- 7VV · (6S)-6-[(2-fluoro-5-methoxyphenyl)methyl]-1-(propan-2-yl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.77 | 0.85 | 40 | empty |
| 2 | 91 | 0.54 | 0.84 | 14 | 7VV |
| 3 | 67 | 0.35 | 0.76 | 17 | empty |
Compared structures
- 5U5H · Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8… · the same entry in another collection · chain A against A, TM-score 1.00
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5U5H · PDBe 5U5H · UniProt O75530
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