Chlorine in PDB 7zzw: Ligand Binding to HDAC2

All present enzymatic activity of Ligand Binding to HDAC2:
3.5.1.98;

The structure of Ligand Binding to HDAC2, PDB code: 7zzw was solved by A.Cleasby, D.Tisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.41 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.149, 97.934, 139.538, 90, 90, 90
R / Rfree (%)	16.4 / 18.9

The structure of Ligand Binding to HDAC2 also contains other interesting chemical elements:

Zinc	(Zn)	3 atoms
Calcium	(Ca)	3 atoms
Sodium	(Na)	3 atoms

The binding sites of Chlorine atom in the Ligand Binding to HDAC2 (pdb code 7zzw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ligand Binding to HDAC2, PDB code: 7zzw:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:19.0 occ:0.71 CL29 A:KKW609 0.0 19.0 0.7 C21 A:KKW609 1.7 15.3 0.7 C22 A:KKW609 2.7 13.6 0.7 C20 A:KKW609 2.7 16.8 0.7 OH A:TYR29 3.1 22.2 1.0 O A:PHE155 3.5 23.2 1.0 CE A:MET35 3.7 24.2 1.0 CG A:MET35 3.8 23.1 1.0 CZ A:TYR29 3.9 22.8 1.0 SD A:MET35 3.9 25.6 1.0 C02 A:KKW609 4.0 12.4 0.7 C19 A:KKW609 4.0 12.5 0.7 CD2 A:LEU144 4.0 25.8 1.0 CB A:PHE155 4.1 21.0 1.0 CG A:LEU144 4.2 22.6 1.0 C A:PHE155 4.2 21.7 1.0 C03 A:KKW609 4.5 12.0 0.7 CE1 A:TYR29 4.5 23.1 1.0 CZ A:PHE114 4.6 28.5 1.0 O A:HOH807 4.6 27.1 1.0 CE2 A:PHE114 4.7 28.9 1.0 CE2 A:TYR29 4.7 22.4 1.0 O A:HOH850 4.7 24.3 1.0 CD1 A:LEU144 4.8 23.5 1.0 CA A:PHE155 4.9 21.9 1.0 CB A:MET35 4.9 22.6 1.0 SG A:CYS156 4.9 19.0 1.0 N A:CYS156 5.0 20.9 1.0

Chlorine binding site 2 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl610 b:23.5 occ:0.80 CL29 B:KKW610 0.0 23.5 0.8 C21 B:KKW610 1.7 24.5 0.8 C22 B:KKW610 2.7 17.9 0.8 C20 B:KKW610 2.7 17.1 0.8 OH B:TYR29 3.0 23.7 1.0 CE B:MET35 3.5 26.1 1.0 O B:PHE155 3.5 24.6 1.0 CG B:MET35 3.8 27.9 1.0 SD B:MET35 3.9 28.6 1.0 CZ B:TYR29 3.9 24.2 1.0 C02 B:KKW610 4.0 21.8 0.8 C19 B:KKW610 4.0 15.9 0.8 CD2 B:LEU144 4.1 25.7 1.0 CB B:PHE155 4.1 23.5 1.0 C B:PHE155 4.3 24.2 1.0 CG B:LEU144 4.3 22.0 1.0 CZ B:PHE114 4.3 27.6 1.0 C03 B:KKW610 4.5 17.2 0.8 CE2 B:PHE114 4.5 28.0 1.0 CE1 B:TYR29 4.5 24.8 1.0 O B:HOH814 4.6 24.9 1.0 O B:HOH852 4.7 23.0 1.0 CE2 B:TYR29 4.7 25.4 1.0 CB B:MET35 4.9 27.7 1.0 CA B:PHE155 4.9 24.0 1.0 CD1 B:LEU144 5.0 25.4 1.0 SG B:CYS156 5.0 22.1 1.0

Chlorine binding site 3 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl608 b:33.4 occ:0.91 CL29 C:KKW608 0.0 33.4 0.9 C21 C:KKW608 1.7 34.3 0.9 C22 C:KKW608 2.7 26.9 0.9 C20 C:KKW608 2.7 28.2 0.9 OH C:TYR29 3.0 31.6 1.0 CE C:MET35 3.5 40.1 1.0 O C:PHE155 3.5 26.4 1.0 CG C:MET35 3.7 39.0 1.0 SD C:MET35 3.8 38.0 1.0 CZ C:TYR29 3.9 33.2 1.0 CD2 C:LEU144 3.9 33.0 1.0 C02 C:KKW608 4.0 29.4 0.9 C19 C:KKW608 4.0 21.3 0.9 CB C:PHE155 4.1 28.7 1.0 CG C:LEU144 4.2 26.8 1.0 C C:PHE155 4.3 27.1 1.0 CZ C:PHE114 4.4 35.8 1.0 C03 C:KKW608 4.5 25.2 0.9 CE2 C:PHE114 4.5 36.4 1.0 CE1 C:TYR29 4.5 33.0 1.0 O C:HOH774 4.6 31.4 1.0 CE2 C:TYR29 4.6 34.4 1.0 O C:HOH791 4.7 37.6 1.0 CB C:MET35 4.8 38.1 1.0 CD1 C:LEU144 4.9 33.8 1.0 CA C:PHE155 4.9 26.9 1.0

E.Tamanini, S.Miyamura, I.M.Buck, B.D.Cons, L.Dawson, C.East, T.Futamura, S.Goto, C.Griffiths-Jones, T.Hashimoto, T.D.Heightman, S.Ishikawa, H.Ito, Y.Kaneko, T.Kawato, K.Kondo, N.Kurihara, J.M.Mccarthy, Y.Mori, T.Nagase, Y.Nakaishi, J.Reeks, A.Sato, P.Schopf, K.Tai, T.Tamai, D.Tisi, A.J.Woolford. Fragment-Based Discovery of A Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. V. 13 1591 2022.
ISSN: ISSN 1948-5875
PubMed: 36262388
DOI: 10.1021/ACSMEDCHEMLETT.2C00272