Potassium in PDB 6r0k: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208, PDB code: 6r0k was solved by C.Barinka, K.Ustinova, L.Motlova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.94 / 1.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.028, 93.886, 51.679, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 17.8

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Potassium atom in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 (pdb code 6r0k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208, PDB code: 6r0k:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2002 b:13.6 occ:1.00 O A:ASP612 2.5 11.7 1.0 OD1 A:ASP610 2.6 12.7 1.0 O A:LEU634 2.6 12.4 1.0 O A:HIS614 2.7 12.3 1.0 OG A:SER633 2.7 12.7 1.0 O A:ASP610 2.8 11.4 1.0 CG A:ASP610 3.2 11.6 1.0 C A:ASP610 3.5 11.0 1.0 C A:ASP612 3.6 11.1 1.0 C A:HIS614 3.6 11.6 1.0 C A:LEU634 3.7 11.9 1.0 CB A:ASP610 3.8 11.9 1.0 N A:ASP612 3.9 11.7 1.0 CB A:SER633 3.9 12.7 1.0 N A:LEU634 3.9 11.6 1.0 CB A:HIS635 4.0 11.7 1.0 OD2 A:ASP610 4.0 12.4 1.0 CA A:ASP612 4.1 11.3 1.0 N A:TRP611 4.2 11.6 1.0 CA A:ASP610 4.2 11.7 1.0 C A:TRP611 4.2 11.5 1.0 CB A:ASP612 4.2 11.8 1.0 CA A:SER633 4.3 12.0 1.0 CA A:HIS615 4.3 11.3 1.0 ND1 A:HIS635 4.3 12.2 1.0 CA A:TRP611 4.3 12.1 1.0 N A:HIS614 4.4 11.2 1.0 N A:HIS615 4.4 11.4 1.0 CA A:HIS635 4.4 11.9 1.0 O A:HOH2125 4.5 13.5 1.0 CA A:LEU634 4.5 11.7 1.0 C A:SER633 4.5 11.6 1.0 N A:HIS635 4.5 11.4 1.0 N A:GLY616 4.5 11.4 1.0 C A:VAL613 4.6 10.8 1.0 CG A:HIS635 4.6 11.7 1.0 CA A:HIS614 4.6 11.2 1.0 N A:VAL613 4.7 10.9 1.0 CE1 A:HIS573 4.7 13.4 1.0 OH A:TYR631 4.7 12.6 1.0 C A:HIS615 4.7 11.3 1.0 O A:TRP611 4.9 11.6 1.0 ND1 A:HIS573 4.9 13.2 1.0

Potassium binding site 2 out of 2 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 within 5.0Å range: probe atom residue distance (Å) B Occ A:K2003 b:13.5 occ:1.00 O A:VAL629 2.7 15.1 1.0 O A:HOH2212 2.7 14.8 1.0 O A:PHE623 2.8 13.4 1.0 O A:TYR662 2.8 12.9 1.0 O A:ASP626 2.9 17.8 1.0 O A:HOH2254 2.9 13.1 1.0 C A:TYR662 3.6 13.3 1.0 CB A:TYR662 3.7 15.3 1.0 C A:PHE623 3.7 14.2 1.0 CB A:PHE623 3.7 13.9 1.0 C A:VAL629 3.9 13.8 1.0 C A:ASP626 4.1 16.9 1.0 CA A:TYR662 4.2 13.8 1.0 N A:TYR631 4.3 12.8 1.0 CA A:PHE623 4.3 13.6 1.0 N A:ASP626 4.4 17.2 1.0 N A:ASN663 4.4 12.6 1.0 CB A:ASP626 4.5 16.7 0.5 CB A:ASP626 4.5 19.1 0.5 CA A:LEU630 4.6 12.9 1.0 CA A:ASP626 4.6 17.4 0.5 N A:GLU624 4.6 14.4 1.0 CA A:ASP626 4.6 16.7 0.5 CA A:GLU624 4.6 15.0 1.0 C A:GLU624 4.7 15.9 1.0 N A:LEU630 4.7 13.8 1.0 O A:GLU624 4.7 15.6 1.0 CB A:TYR631 4.7 12.2 1.0 CB A:ASN663 4.8 12.2 1.0 CA A:ASN663 4.8 12.5 1.0 C A:LEU630 4.9 12.8 1.0 O A:GLY659 4.9 17.2 1.0 CA A:VAL629 4.9 14.2 1.0 CG A:PHE623 5.0 14.1 1.0 OD1 A:ASN663 5.0 12.9 1.0

S.Shen, M.Hadley, K.Ustinova, J.Pavlicek, T.Knox, S.Noonepalle, M.T.Tavares, C.A.Zimprich, G.Zhang, M.B.Robers, C.Barinka, A.P.Kozikowski, A.Villagra. Discovery of A New Isoxazole-3-Hydroxamate-Based Histone Deacetylase 6 Inhibitor Ss-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models. J.Med.Chem. V. 62 8557 2019.
ISSN: ISSN 0022-2623
PubMed: 31414801
DOI: 10.1021/ACS.JMEDCHEM.9B00946