Sodium in PDB 4yh4: Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D)

The structure of Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D), PDB code: 4yh4 was solved by D.Lakshminarasimhan, A.White, R.K.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.96 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.799, 44.436, 77.353, 90.00, 90.00, 90.00
R / Rfree (%)	10.7 / 14.7

The binding sites of Sodium atom in the Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D) (pdb code 4yh4). 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 Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D), PDB code: 4yh4:

Sodium binding site 1 out of 1 in the Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human BRD4(1) in Complex with 4-[(5- Phenylpyridin-3-Yl)Carbonyl]-3,4-Dihydroquinoxalin-2(1H)-One (Compound 19D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:11.2 occ:1.00 O A:ASN140 2.7 15.0 1.0 O A:TYR137 2.8 9.9 1.0 O A:ILE138 2.8 10.5 1.0 C A:ILE138 3.5 9.1 1.0 O A:HOH459 3.8 17.6 1.0 C A:ASN140 3.8 11.6 1.0 CA A:ILE138 3.9 8.4 0.5 CA A:ILE138 3.9 8.5 0.5 C A:TYR137 3.9 7.9 1.0 N A:ASN140 4.2 9.4 1.0 O A:HOH421 4.2 45.1 1.0 N A:ILE138 4.4 7.5 1.0 C A:TYR139 4.4 8.9 1.0 N A:TYR139 4.4 8.5 1.0 CA A:ASN140 4.6 9.8 1.0 N A:LYS141 4.7 16.4 1.0 CA A:LYS141 4.7 15.6 1.0 O A:TYR139 4.8 11.3 1.0 CA A:TYR139 4.9 9.2 1.0

B.C.Duffy, S.Liu, G.S.Martin, R.Wang, M.M.Hsia, H.Zhao, C.Guo, M.Ellis, J.F.Quinn, O.A.Kharenko, K.Norek, E.M.Gesner, P.R.Young, K.G.Mclure, G.S.Wagner, D.Lakshminarasimhan, A.White, R.K.Suto, H.C.Hansen, D.B.Kitchen. Discovery of A New Chemical Series of BRD4(1) Inhibitors Using Protein-Ligand Docking and Structure-Guided Design. Bioorg.Med.Chem.Lett. V. 25 2818 2015.
ISSN: ESSN 1464-3405
PubMed: 26022843
DOI: 10.1016/J.BMCL.2015.04.107