Research workbench
Crystal structure of eed in complex with 3-(3-METHOXYBENZYL)PIPERIDINE hydrochloride
Analyse Crystal structure of eed in complex with 3-(3-METHOXYBENZYL)PIPERIDINE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U5K
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed
- UniProt
- O75530
- Ligands
- 7VY
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 358 | 3% helix, 47% strand | O75530 |
Ligands and binding sites
- 7VY · (3R)-3-[(3-methoxyphenyl)methyl]piperidine · ligand · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.76 | 0.85 | 50 | empty |
| 2 | 93 | 0.55 | 0.85 | 12 | 7VY |
| 3 | 76 | 0.34 | 0.75 | 17 | empty |
| 4 | 56 | 0.27 | 0.73 | 12 | empty |
Compared structures
- 5U5K · Crystal structure of EED in complex with 3-(3-methoxybenzyl)piperidine hydrochloride · 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 5U5K · PDBe 5U5K · UniProt O75530
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