Chlorine 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:

Potassium	(K)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl2004 b:22.2 occ:0.50 CL1 A:JNN2004 0.0 22.2 0.5 CL1 A:JNN2004 0.1 40.9 0.5 C11 A:JNN2004 1.7 36.2 0.5 C11 A:JNN2004 1.7 20.7 0.5 C10 A:JNN2004 2.7 35.3 0.5 C10 A:JNN2004 2.7 19.3 0.5 C12 A:JNN2004 2.7 21.6 0.5 C12 A:JNN2004 2.7 35.5 0.5 CL2 A:JNN2004 3.1 25.1 0.5 CL2 A:JNN2004 3.2 37.8 0.5 CD A:PRO464 3.7 14.5 1.0 C9 A:JNN2004 4.0 33.9 0.5 C13 A:JNN2004 4.0 35.4 0.5 C9 A:JNN2004 4.0 20.9 0.5 C13 A:JNN2004 4.0 20.9 0.5 O A:HOH2492 4.0 39.7 1.0 CG A:PRO464 4.0 15.9 1.0 C8 A:JNN2004 4.5 33.3 0.5 C8 A:JNN2004 4.5 20.3 0.5

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl2004 b:40.9 occ:0.50 CL1 A:JNN2004 0.0 40.9 0.5 CL1 A:JNN2004 0.1 22.2 0.5 C11 A:JNN2004 1.7 36.2 0.5 C11 A:JNN2004 1.7 20.7 0.5 C10 A:JNN2004 2.7 35.3 0.5 C10 A:JNN2004 2.7 19.3 0.5 C12 A:JNN2004 2.7 21.6 0.5 C12 A:JNN2004 2.7 35.5 0.5 CL2 A:JNN2004 3.2 25.1 0.5 CL2 A:JNN2004 3.2 37.8 0.5 CD A:PRO464 3.7 14.5 1.0 CG A:PRO464 4.0 15.9 1.0 O A:HOH2492 4.0 39.7 1.0 C9 A:JNN2004 4.0 33.9 0.5 C9 A:JNN2004 4.0 20.9 0.5 C13 A:JNN2004 4.0 20.9 0.5 C13 A:JNN2004 4.0 35.4 0.5 C8 A:JNN2004 4.5 33.3 0.5 C8 A:JNN2004 4.5 20.3 0.5 CB A:PRO464 5.0 15.7 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl2004 b:25.1 occ:0.50 CL2 A:JNN2004 0.0 25.1 0.5 C12 A:JNN2004 1.7 21.6 0.5 C10 A:JNN2004 1.7 35.3 0.5 C9 A:JNN2004 2.7 33.9 0.5 C13 A:JNN2004 2.7 20.9 0.5 C11 A:JNN2004 2.7 36.2 0.5 C11 A:JNN2004 2.7 20.7 0.5 CL1 A:JNN2004 3.1 22.2 0.5 CL1 A:JNN2004 3.2 40.9 0.5 CD1 A:LEU712 3.8 18.5 1.0 CG A:LEU712 3.9 17.0 1.0 C8 A:JNN2004 3.9 33.3 0.5 C12 A:JNN2004 4.0 35.5 0.5 C8 A:JNN2004 4.0 20.3 0.5 C10 A:JNN2004 4.0 19.3 0.5 O A:HOH2261 4.3 29.4 1.0 C13 A:JNN2004 4.4 35.4 0.5 CD2 A:LEU712 4.4 19.1 1.0 C9 A:JNN2004 4.5 20.9 0.5

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl2004 b:37.8 occ:0.50 CL2 A:JNN2004 0.0 37.8 0.5 C12 A:JNN2004 1.7 35.5 0.5 C10 A:JNN2004 1.8 19.3 0.5 C13 A:JNN2004 2.7 35.4 0.5 C9 A:JNN2004 2.7 20.9 0.5 C11 A:JNN2004 2.7 20.7 0.5 C11 A:JNN2004 2.7 36.2 0.5 CL1 A:JNN2004 3.2 22.2 0.5 CL1 A:JNN2004 3.2 40.9 0.5 CD2 A:HIS463 3.5 15.4 1.0 CD A:PRO464 3.8 14.5 1.0 OD2 A:ASP460 3.9 23.2 1.0 C12 A:JNN2004 4.0 21.6 0.5 C8 A:JNN2004 4.0 20.3 0.5 C8 A:JNN2004 4.0 33.3 0.5 O A:HOH2335 4.0 28.7 1.0 C10 A:JNN2004 4.0 35.3 0.5 NE2 A:HIS463 4.0 14.6 1.0 CG A:HIS463 4.1 14.8 1.0 C13 A:JNN2004 4.5 20.9 0.5 CA A:HIS463 4.5 15.1 1.0 C9 A:JNN2004 4.5 33.9 0.5 CB A:HIS463 4.6 14.3 1.0 CG A:PRO464 4.7 15.9 1.0 CE1 A:HIS463 4.8 15.1 1.0 ND1 A:HIS463 4.8 14.5 1.0 N A:PRO464 5.0 14.3 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