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N-terminal bromodomain of human BRD2 in complex with 4,4'-(quinoline- 5,7-DIYL)BIS(3,5-dimethylisoxazole) inhibitor

Analyse N-terminal bromodomain of human BRD2 in complex with 4,4'-(quinoline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MO8
Type: protein
Length: 327 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: JWD, SO4
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	114	58% helix, 2% strand	P25440
B	Bromodomain-containing protein 2	protein	107	65% helix, 0% strand	P25440
C	Bromodomain-containing protein 2	protein	106	64% helix, 0% strand	P25440

Ligands and binding sites

JWD · 5,7-bis(3,5-dimethyl-1,2-oxazol-4-yl)quinoline · ligand · 3 copies · chains A, C, B
SO4 · Sulfate ion · ion · chains B

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	428	0.74	0.84	48	JWD
2	145	0.54	0.80	20	JWD
3	118	0.52	0.81	19	JWD
4	97	0.35	0.74	17	empty
5	87	0.35	0.75	18	empty

Interfaces

3 interfaces between chains.

A–B · 1081 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 337 Å² buried · 1 hydrogen bond · protein-protein
B–C · 60 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MO8 · N-terminal bromodomain of human BRD2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain B 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 P25440
Elsewhere: RCSB PDB 6MO8 · PDBe 6MO8 · UniProt P25440

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