Sodium in PDB 5d3t: First Bromodomain of BRD4 Bound to Inhibitor XD47

The structure of First Bromodomain of BRD4 Bound to Inhibitor XD47, PDB code: 5d3t was solved by D.Wohlwend, M.Huegle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.20 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.440, 42.730, 79.500, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.1

The binding sites of Sodium atom in the First Bromodomain of BRD4 Bound to Inhibitor XD47 (pdb code 5d3t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the First Bromodomain of BRD4 Bound to Inhibitor XD47, PDB code: 5d3t:

Sodium binding site 1 out of 1 in the First Bromodomain of BRD4 Bound to Inhibitor XD47


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of First Bromodomain of BRD4 Bound to Inhibitor XD47 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:49.7 occ:1.00 O A:ASN140 2.7 23.2 1.0 O A:ILE138 3.0 19.1 1.0 O A:TYR137 3.4 17.6 1.0 C A:ASN140 3.7 22.2 1.0 C A:ILE138 3.8 17.8 1.0 O A:HOH358 4.0 19.3 1.0 O A:HOH426 4.3 44.1 1.0 N A:ASN140 4.4 18.2 1.0 CA A:ILE138 4.4 18.1 1.0 C A:TYR139 4.4 18.3 1.0 C A:TYR137 4.4 16.8 1.0 CA A:LYS141 4.5 26.8 1.0 N A:LYS141 4.5 24.6 1.0 O A:TYR139 4.5 19.3 1.0 O A:HOH313 4.5 34.5 1.0 CD A:PRO142 4.6 30.5 1.0 CA A:ASN140 4.7 19.6 1.0 N A:TYR139 4.7 16.5 1.0 N A:ILE138 4.9 16.5 1.0

M.Hugle, X.Lucas, G.Weitzel, D.Ostrovskyi, B.Breit, S.Gerhardt, O.Einsle, S.Gunther, D.Wohlwend. 4-Acyl Pyrrole Derivatives Yield Novel Vectors For Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1). J.Med.Chem. V. 59 1518 2016.
ISSN: ISSN 0022-2623
PubMed: 26731611
DOI: 10.1021/ACS.JMEDCHEM.5B01267