MolNFT v1 · #116493 · protein

Crystal structure of BRD2(BD2) W370F mutant with ligand 28 bound

5DFD · Bromodomain-containing protein 2: “Crystal structure of BRD2(BD2) W370F mutant with ligand 28 bound”. X-ray diffraction, 1 ligand (59E), 1 pocket (best druggability 0.45). MolNFT v1 #116493 on GenesisL1: 3D structure, binding sites…

PDB: 5DFD
Type: protein
Length: 108 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 2
UniProt: P25440
Ligands: 59E
Pockets: 1 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 2	protein	108	70% helix, 0% strand	P25440

Ligands and binding sites

59E · methyl [(4S)-6-(1H-indol-4-yl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]acetate · ligand · chains A
GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.45	0.80	18	59E

Compared structures

5DFD · Crystal structure of BRD2(BD2) W370F mutant with ligand 28 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 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 5DFD · PDBe 5DFD · UniProt P25440

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