Research workbench

Crystal structure of BCL6 BTB domain with compound 15f

Analyse Crystal structure of BCL6 BTB domain with compound 15f in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C3L
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.46092
Source: Homo sapiens
Molecule: B-cell lymphoma 6 protein
UniProt: P41182
Ligands: EGP
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · resolution 1.46092 · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	B-cell lymphoma 6 protein	protein	124	53% helix, 14% strand	P41182

Ligands and binding sites

EGP · N-[2-(1H-indol-3-yl)ethyl]-N'-{3-[(4-methylpiperazin-1-yl)methyl]-1-[2-(morpholin-4-yl)-2-oxoethyl]-1H-indol-6-yl}thiourea · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	148	0.49	0.78	23	EGP
2	129	0.44	0.76	23	EGP
3	104	0.35	0.74	29	empty

Interfaces

1 interface between chains.

A–B · 1789 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6C3L · Crystal structure of BCL6 btb domain with compound 15F · the same entry in another collection · chain A against A, 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 B 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 6C3L · PDBe 6C3L · UniProt P41182

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.