Research workbench

BRD2_BROMODOMAIN2 complex with inhibitor 744

Analyse BRD2_BROMODOMAIN2 complex with inhibitor 744 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E6J
Type: protein
Length: 654 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: HWV
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Bromodomain-containing protein 2	protein	109	72% helix, 0% strand	P25440

Ligands and binding sites

HWV · N-ethyl-4-[2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl]-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.81	0.82	86	HWV
2	642	0.78	0.83	66	HWV
3	551	0.76	0.82	58	HWV
4	112	0.48	0.80	23	empty
5	93	0.44	0.80	20	empty

Interfaces

9 interfaces between chains.

A–D · 614 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 405 Å² buried · 1 hydrogen bond · protein-protein
C–D · 381 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 369 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 356 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6E6J · BRD2_Bromodomain2 complex with inhibitor 744 · the same entry in another collection · chain F against F, TM-score 1.00
P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P25440
Elsewhere: RCSB PDB 6E6J · PDBe 6E6J · UniProt P25440

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