MolNFT v1 · #168164 · protein

Structure of eed bound to inhibitor 5285

6W7F · Polycomb protein eed: “Structure of eed bound to inhibitor 5285”. X-ray diffraction, 1 ligand (Q3D), 3 pockets (best druggability 0.77). MolNFT v1 #168164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W7F
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: Q3D
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polycomb protein eed	protein	359	5% helix, 47% strand	O75530

Ligands and binding sites

Q3D · 8-(6-cyclopropylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1, 5-c]pyrimidin-5-amine · ligand · 2 copies · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.77	0.86	37	empty
2	73	0.58	0.88	10	Q3D
3	84	0.35	0.75	15	empty

Compared structures

6W7F · Structure of EED bound to inhibitor 5285 · 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 6W7F · PDBe 6W7F · UniProt O75530

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