Chlorine in PDB 7kbg: Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)

All present enzymatic activity of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20):
3.5.1.98;

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg was solved by D.J.Klein, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.08 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.26, 99.27, 139.02, 90, 90, 90
R / Rfree (%)	18.4 / 19.6

The structure of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Zinc	(Zn)	3 atoms
Fluorine	(F)	3 atoms

The binding sites of Chlorine atom in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) (pdb code 7kbg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20), PDB code: 7kbg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl411 b:26.4 occ:1.00 CL1 C:WBD411 0.0 26.4 1.0 C4 C:WBD411 1.7 27.3 1.0 C3 C:WBD411 2.7 27.6 1.0 C5 C:WBD411 2.7 28.2 1.0 O B:HOH847 2.9 56.7 1.0 O C:LYS67 3.0 15.6 1.0 CB B:ASP341 3.6 14.5 1.0 CD1 C:LEU162 3.9 16.3 1.0 CD1 C:TYR68 3.9 14.5 1.0 C1 C:WBD411 3.9 28.6 1.0 C6 C:WBD411 4.0 28.8 1.0 CA B:ASP341 4.0 13.2 1.0 C C:LYS67 4.1 14.4 1.0 CA C:TYR68 4.2 14.0 1.0 C C:WBD411 4.5 28.8 1.0 O B:ASP341 4.5 13.4 1.0 CD2 C:LEU162 4.6 17.1 1.0 N C:TYR68 4.6 13.7 1.0 CB C:TYR68 4.7 14.1 1.0 CE1 C:TYR68 4.7 15.5 1.0 CE B:LYS343 4.7 15.4 1.0 CG C:TYR68 4.8 14.2 1.0 CG B:LYS343 4.8 12.6 1.0 C B:ASP341 4.8 12.4 1.0 CG C:LEU162 4.9 15.8 1.0

Chlorine binding site 2 out of 2 in the Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human HDAC2 in Complex with A 2-Substituted Benzamide Inhibitor (Compound 20) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl411 b:32.4 occ:1.00 CL C:WBD411 0.0 32.4 1.0 C2 C:WBD411 1.6 30.4 1.0 N1 C:WBD411 2.6 29.5 1.0 N C:WBD411 2.7 29.4 1.0 OG1 C:THR191 3.6 15.8 1.0 C C:WBD411 3.8 28.8 1.0 C1 C:WBD411 3.8 28.6 1.0 O C:HOH817 3.9 44.8 1.0 O C:HOH685 3.9 38.1 1.0 CB C:THR191 4.0 14.8 1.0 CG2 C:THR191 4.0 15.2 1.0 O C:HOH791 4.2 38.7 1.0 O C:HOH629 4.3 86.9 1.0 CD1 C:LEU165 4.4 16.3 1.0 O C:HOH737 4.4 25.1 1.0 CB C:ARG193 4.5 15.1 1.0 CG B:PRO340 4.5 15.4 1.0 O A:HOH764 4.5 25.8 1.0 CD C:ARG193 4.7 17.9 1.0 CG C:ARG193 4.8 16.8 1.0 CB B:PRO340 4.9 14.8 1.0 NH2 C:ARG193 4.9 19.4 1.0 CD1 C:PHE188 5.0 13.8 1.0

J.Liu, Y.Yu, J.Kelly, D.Sha, A.B.Alhassan, W.Yu, M.M.Maletic, J.L.Duffy, D.J.Klein, M.K.Holloway, S.Carroll, B.J.Howell, R.J.O.Barnard, S.Wolkenberg, J.A.Kozlowski. Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on A 2-Substituted Benzamide Zinc Binding Group. Acs Med.Chem.Lett. V. 11 2476 2020.
ISSN: ISSN 1948-5875
PubMed: 33335670
DOI: 10.1021/ACSMEDCHEMLETT.0C00462