MolNFT v1 · #169782 · protein

Cryo-EM structure of BCL6 bound to bi-3802

6XMX · B-cell lymphoma 6 protein: “Cryo-EM structure of BCL6 bound to bi-3802”. Electron microscopy, 1 ligand (U52), 9 pockets (best druggability 0.85). MolNFT v1 #169782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XMX
Type: protein
Length: 976 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-cell lymphoma 6 protein
UniProt: P41182
Ligands: U52
Pockets: 9 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 57% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	B-cell lymphoma 6 protein	protein	122	57% helix, 14% strand	P41182

Ligands and binding sites

U52 · 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide · ligand · 8 copies · chains A, B, E, D, C, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1080	0.85	0.86	112	U52
2	1149	0.85	0.86	113	U52
3	781	0.83	0.86	88	U52
4	329	0.73	0.85	40	U52
5	145	0.51	0.79	22	U52

Interfaces

16 interfaces between chains.

A–B · 1628 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1595 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 1555 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1516 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 702 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6XMX · Cryo-EM structure of BCL6 bound to BI-3802 · the same entry in another collection · chain H against H, TM-score 1.00
P41182 · AlphaFold monomer V2.0 prediction for B-cell lymphoma 6 protein (P41182) · a predicted model of the same protein · chain E against A, TM-score 0.32

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 P41182
Elsewhere: RCSB PDB 6XMX · PDBe 6XMX · UniProt P41182

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