MolNFT v1 · #123956 · protein
Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of eed
5K0M · Polycomb protein eed: “Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of eed”. X-ray diffraction, 1 ligand (6PU), 3 pockets (best druggability 0.77). MolNFT v1 #123956 on GenesisL1: 3D structure…
- PDB
- 5K0M
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed
- UniProt
- O75530
- Ligands
- 6PU
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 359 | 6% helix, 47% strand | O75530 |
Ligands and binding sites
- 6PU · (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-{4-[4-(methylsulfonyl)piperazin-1-yl]phenyl}pyrrolidin-3-amine · ligand · 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 | 453 | 0.77 | 0.85 | 40 | empty |
| 2 | 101 | 0.55 | 0.84 | 11 | 6PU |
| 3 | 89 | 0.37 | 0.75 | 14 | empty |
Compared structures
- 5K0M · Targeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED · 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 5K0M · PDBe 5K0M · UniProt O75530
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