MolNFT v1 · #171165 · protein

Eed in complex with a triazolopyrimidine

6YVJ · Polycomb protein eed: “Eed in complex with a triazolopyrimidine”. X-ray diffraction, 2 ligands (L9W, EJR), 7 pockets (best druggability 0.78). MolNFT v1 #171165 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YVJ
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, EJR
Pockets: 7 · best druggability 0.78

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, 48% 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
EJR · N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine · ligand · chains B
GOL · Glycerol · additive · chains B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	514	0.78	0.85	39	GOL
2	483	0.77	0.85	39	empty
3	73	0.57	0.88	10	L9W
4	79	0.57	0.87	11	EJR
5	110	0.39	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 218 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YVJ · EED in complex with a triazolopyrimidine · 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 1.00

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 6YVJ · PDBe 6YVJ · UniProt O75530

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