MolNFT v1 · #159388 · protein

BRD2_BROMODOMAIN1 complex with inhibitor 744

6ONY · Bromodomain-containing protein 2: “BRD2_BROMODOMAIN1 complex with inhibitor 744”. X-ray diffraction, 1 ligand (HWV), 4 pockets (best druggability 0.51). MolNFT v1 #159388 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ONY
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: HWV
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	114	61% helix, 0% strand	P25440
B	Bromodomain-containing protein 2	protein	110	64% 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 · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.51	0.81	19	HWV
2	111	0.48	0.80	19	HWV
3	106	0.41	0.77	19	empty
4	77	0.38	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 1131 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6ONY · BRD2_Bromodomain1 complex with inhibitor 744 · the same entry in another collection · chain B against B, 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 0.99

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 6ONY · PDBe 6ONY · UniProt P25440

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