MolNFT v1 · #108163 · protein

N-terminal bromodomain of human BRD2 with I-BET726 (GSK1324726A)

4UYF · Bromodomain-containing protein 2: “N-terminal bromodomain of human BRD2 with I-BET726 (GSK1324726A)”. X-ray diffraction, 2 ligands (73B, SO4), 5 pockets (best druggability 0.78). MolNFT v1 #108163 on GenesisL1: 3D structure, binding…

PDB: 4UYF
Type: protein
Length: 334 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: 73B, SO4
Pockets: 5 · best druggability 0.78

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	119	59% helix, 2% strand	P25440
B	Bromodomain-containing protein 2	protein	108	66% helix, 0% strand	P25440
C	Bromodomain-containing protein 2	protein	107	63% helix, 0% strand	P25440

Ligands and binding sites

73B · 4-[(2S,4R)-1-acetyl-4-[(4-chlorophenyl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl]benzoic acid · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains A, C, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C

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	709	0.78	0.82	66	SO4, EDO, 73B
2	125	0.51	0.80	22	73B
3	108	0.50	0.81	19	73B
4	83	0.40	0.78	15	EDO
5	86	0.37	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 1022 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 423 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 49 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4UYF · N-Terminal bromodomain of Human BRD2 with I-BET726 (GSK1324726A) · 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 0.98

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 4UYF · PDBe 4UYF · UniProt P25440

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