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Crystal structure of BRD2(BD1)WITH ligand BY27 bound

Analyse Crystal structure of BRD2(BD1)WITH ligand BY27 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K05
Type: protein
Length: 321 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: CQF
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	108	65% helix, 0% strand	P25440
B	Bromodomain-containing protein 2	protein	107	66% helix, 0% strand	P25440
C	Bromodomain-containing protein 2	protein	106	64% helix, 0% strand	P25440

Ligands and binding sites

CQF · (6~{R})-~{N}-(4-chlorophenyl)-1-methyl-8-(1-methylpyrazol-4-yl)-5,6-dihydro-4~{H}-[1,2, 4]triazolo[4,3-a][1]benzazepin-6-amine · ligand · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	209	0.62	0.82	31	empty
2	123	0.51	0.80	19	CQF
3	126	0.48	0.78	20	CQF
4	173	0.46	0.75	22	empty
5	64	0.38	0.79	18	empty

Interfaces

3 interfaces between chains.

A–B · 1094 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 324 Å² buried · 1 hydrogen bond · protein-protein
B–C · 51 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6K05 · Crystal structure of BRD2(BD1)with ligand BY27 bound · 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 6K05 · PDBe 6K05 · UniProt P25440

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