MolNFT v1 · #170055 · protein

Crystal structure of BRD4-BD1 with compound 3

6XV3 · Bromodomain-containing protein 4: “Crystal structure of BRD4-BD1 with compound 3”. X-ray diffraction, 1 ligand (O2B), 8 pockets (best druggability 0.78). MolNFT v1 #170055 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6XV3
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: O2B
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Bromodomain-containing protein 4	protein	127	54% helix, 0% strand	O60885

Ligands and binding sites

O2B · 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine · ligand · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.78	0.80	89	empty
2	364	0.69	0.82	42	empty
3	297	0.57	0.77	31	empty
4	136	0.56	0.82	25	O2B
5	118	0.55	0.83	27	empty

Interfaces

5 interfaces between chains.

B–C · 613 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 409 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 344 Å² buried · 1 hydrogen bond · protein-protein
A–B · 292 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 79 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6XV3 · Crystal structure of BRD4-BD1 with compound 3 · 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 D 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 6XV3 · PDBe 6XV3 · UniProt O60885

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