MolNFT v1 · #101953 · protein

Crystal structure of the first bromodomain of human BRD4 in complex with TG101209

4O76 · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of human BRD4 in complex with TG101209”. X-ray diffraction, 1 ligand (1M3), 6 pockets (best druggability 0.77). MolNFT v1 #101953 on GenesisL1: 3D…

PDB: 4O76
Type: protein
Length: 508 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 4
UniProt: O60885
Ligands: 1M3
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Bromodomain-containing protein 4	protein	127	55% helix, 0% strand	O60885

Ligands and binding sites

1M3 · N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	849	0.77	0.80	62	1M3
2	874	0.76	0.79	58	1M3
3	254	0.62	0.81	26	empty
4	263	0.52	0.75	33	empty
5	131	0.39	0.74	22	empty

Interfaces

4 interfaces between chains.

A–C · 291 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 269 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 209 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 180 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4O76 · Crystal structure of the first bromodomain of human BRD4 in complex with TG101209 · the same entry in another collection · chain D against D, TM-score 1.00
O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain C 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 O60885
Elsewhere: RCSB PDB 4O76 · PDBe 4O76 · UniProt O60885

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