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Crystal structure of the human BRD2 BD1 bromodomain in complex with a tetrahydroquinoline analogue

Analyse Crystal structure of the human BRD2 BD1 bromodomain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DDI
Type: protein
Length: 329 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: G7V, 03S, SO4
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	115	61% helix, 2% strand	P25440
B, C	Bromodomain-containing protein 2	protein	107	65% helix, 0% strand	P25440

Ligands and binding sites

G7V · 4-{[(2S,4R)-1-acetyl-2-methyl-6-(1H-pyrazol-3-yl)-1,2, 3,4-tetrahydroquinolin-4-yl]amino}benzonitrile · ligand · 3 copies · chains A, B, C
03S · methanesulfonic acid · ligand · chains B
SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

5 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	596	0.73	0.80	63	G7V
2	131	0.53	0.81	22	G7V
3	105	0.52	0.82	18	G7V
4	75	0.40	0.79	18	empty
5	69	0.35	0.76	15	empty

Interfaces

2 interfaces between chains.

A–B · 1073 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 304 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6DDI · Crystal Structure of the human BRD2 BD1 bromodomain in complex with a Tetrahydroquinoline… · 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 6DDI · PDBe 6DDI · UniProt P25440

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