Zinc in PDB 5mat: Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor

The structure of Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor, PDB code: 5mat was solved by S.Moniot, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.89 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.683, 68.560, 78.462, 90.00, 95.66, 90.00
R / Rfree (%)	16.5 / n/a

The binding sites of Zinc atom in the Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor (pdb code 5mat). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor, PDB code: 5mat:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:19.3 occ:1.00 SG A:CYS221 2.3 19.7 1.0 SG A:CYS224 2.3 21.7 1.0 SG A:CYS195 2.4 19.8 1.0 SG A:CYS200 2.4 23.8 1.0 HB3 A:CYS200 2.9 30.4 1.0 HB3 A:CYS221 3.1 22.4 1.0 CB A:CYS221 3.1 18.7 1.0 HB2 A:CYS195 3.1 24.1 1.0 CB A:CYS200 3.1 25.4 1.0 HB2 A:CYS221 3.1 22.4 1.0 CB A:CYS195 3.2 20.1 1.0 H A:CYS224 3.3 28.1 1.0 HB3 A:CYS195 3.3 24.1 1.0 HB2 A:CYS200 3.4 30.4 1.0 HB3 A:CYS224 3.5 27.1 1.0 CB A:CYS224 3.6 22.6 1.0 HB2 A:ASP223 3.6 35.7 1.0 HB2 A:SER226 3.7 26.7 1.0 H A:HIS202 3.8 26.9 1.0 N A:CYS224 3.9 23.4 1.0 HB3 A:SER197 3.9 31.8 1.0 H A:SER226 4.0 27.2 1.0 HB2 A:HIS202 4.1 32.2 1.0 HB3 A:HIS202 4.1 32.2 1.0 H A:ARG201 4.1 30.6 1.0 CA A:CYS224 4.3 22.7 1.0 HB2 A:CYS224 4.3 27.1 1.0 H A:ASP223 4.4 29.1 1.0 CA A:CYS200 4.5 26.5 1.0 CB A:HIS202 4.5 26.9 1.0 CB A:ASP223 4.6 29.8 1.0 CA A:CYS221 4.6 22.6 1.0 N A:ARG201 4.6 25.5 1.0 CB A:SER226 4.6 22.2 1.0 HH A:TYR204 4.6 29.8 1.0 CA A:CYS195 4.7 21.0 1.0 O A:HOH573 4.7 28.0 1.0 N A:HIS202 4.7 22.4 1.0 H A:GLN225 4.7 27.6 1.0 H A:SER197 4.7 31.7 1.0 HG A:SER226 4.8 28.0 1.0 C A:CYS224 4.8 22.7 1.0 N A:SER226 4.8 22.6 1.0 CB A:SER197 4.8 26.5 1.0 C A:CYS200 4.8 26.4 1.0 HB3 A:ASP223 4.8 35.7 1.0 C A:ASP223 4.9 25.5 1.0 HA A:CYS221 4.9 27.1 1.0 N A:GLN225 4.9 23.0 1.0 HA A:CYS195 4.9 25.2 1.0 HB2 A:SER197 5.0 31.8 1.0

Zinc binding site 2 out of 2 in the Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Sirtuin 2 in Complex with A Selective Thienopyrimidinone Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:65.0 occ:1.00 SG C:CYS200 2.2 66.8 1.0 SG C:CYS195 2.4 65.3 1.0 SG C:CYS221 2.5 55.2 1.0 SG C:CYS224 2.5 60.7 1.0 HB3 C:CYS200 2.6 96.6 1.0 CB C:CYS200 2.8 80.5 1.0 HB2 C:CYS221 3.0 66.5 1.0 HB2 C:CYS195 3.0 73.3 1.0 HB2 C:CYS200 3.0 96.6 1.0 HB3 C:CYS221 3.0 66.5 1.0 CB C:CYS221 3.1 55.4 1.0 CB C:CYS195 3.1 61.1 1.0 HB3 C:CYS195 3.1 73.3 1.0 H C:CYS224 3.5 85.5 1.0 HB2 C:ASP223 3.6 90.5 1.0 HB3 C:CYS224 3.7 80.2 1.0 CB C:CYS224 3.7 66.8 1.0 H C:HIS202 3.8 82.7 1.0 HB3 C:SER197 3.9 72.3 1.0 HB2 C:HIS202 3.9 89.8 1.0 HB3 C:SER226 4.0 80.4 1.0 HB3 C:HIS202 4.0 89.8 1.0 N C:CYS224 4.1 71.2 1.0 H C:SER226 4.2 75.9 1.0 H C:ARG201 4.3 84.5 1.0 CA C:CYS200 4.3 79.1 1.0 CB C:HIS202 4.4 74.9 1.0 CA C:CYS224 4.4 69.4 1.0 H C:ASP223 4.5 84.2 1.0 HB2 C:CYS224 4.5 80.2 1.0 CB C:ASP223 4.6 75.5 1.0 HH C:TYR204 4.6 68.1 1.0 CA C:CYS221 4.6 55.9 1.0 CA C:CYS195 4.6 57.2 1.0 N C:HIS202 4.6 68.9 1.0 N C:ARG201 4.6 70.4 1.0 HA C:CYS200 4.7 94.9 1.0 C C:CYS200 4.7 75.2 1.0 CB C:SER226 4.8 67.0 1.0 H C:GLN225 4.8 81.0 0.6 H C:GLN225 4.8 81.0 0.4 CB C:SER197 4.8 60.2 1.0 HB2 C:SER226 4.9 80.4 1.0 HA C:CYS221 4.9 67.1 1.0 HB3 C:ASP223 4.9 90.5 1.0 HA C:CYS195 4.9 68.7 1.0 HE2 C:TYR204 4.9 62.1 1.0 H C:SER197 4.9 73.4 1.0 C C:ASP223 5.0 73.7 1.0 C C:CYS224 5.0 68.2 1.0 N C:SER226 5.0 63.3 1.0

S.Sundriyal, S.Moniot, Z.Mahmud, S.Yao, P.Di Fruscia, C.R.Reynolds, D.T.Dexter, M.J.Sternberg, E.W.Lam, C.Steegborn, M.J.Fuchter. Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket. J. Med. Chem. V. 60 1928 2017.
ISSN: ISSN 1520-4804
PubMed: 28135086
DOI: 10.1021/ACS.JMEDCHEM.6B01690