Zinc in PDB 6aa5: Crystal Structure of MTH1 in Complex with 3-Isomangostin

All present enzymatic activity of Crystal Structure of MTH1 in Complex with 3-Isomangostin:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of MTH1 in Complex with 3-Isomangostin, PDB code: 6aa5 was solved by T.Yokoyama, R.Kitakami, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 1.90
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.086, 67.086, 141.016, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.8

The binding sites of Zinc atom in the Crystal Structure of MTH1 in Complex with 3-Isomangostin (pdb code 6aa5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of MTH1 in Complex with 3-Isomangostin, PDB code: 6aa5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of MTH1 in Complex with 3-Isomangostin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MTH1 in Complex with 3-Isomangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:22.7 occ:1.00 OD2 A:ASP82 1.9 26.1 1.0 ND1 A:HIS159 2.0 22.3 1.0 NE2 A:HIS161 2.0 20.9 1.0 NE2 A:HIS84 2.0 20.6 1.0 CG A:ASP82 2.8 23.1 1.0 CE1 A:HIS84 2.9 23.5 1.0 CE1 A:HIS159 3.0 22.0 1.0 CE1 A:HIS161 3.0 20.0 1.0 OD1 A:ASP82 3.0 19.4 1.0 CG A:HIS159 3.1 24.3 1.0 CD2 A:HIS161 3.1 22.0 1.0 CD2 A:HIS84 3.1 19.3 1.0 CB A:HIS159 3.4 22.6 1.0 CD1 A:LEU6 3.8 20.2 1.0 ND1 A:HIS84 4.1 24.5 1.0 NE2 A:HIS159 4.1 21.9 1.0 ND1 A:HIS161 4.1 23.9 1.0 CD2 A:HIS159 4.2 23.8 1.0 CG A:HIS161 4.2 24.3 1.0 CB A:ASP82 4.2 22.3 1.0 CG A:HIS84 4.2 20.5 1.0 OE1 A:GLN69 4.6 39.8 1.0 CD1 A:ILE45 4.8 30.7 1.0 CA A:HIS159 4.9 23.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of MTH1 in Complex with 3-Isomangostin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MTH1 in Complex with 3-Isomangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:25.1 occ:1.00 OE1 A:GLU41 2.0 26.8 1.0 NE2 A:HIS164 2.0 27.2 1.0 CD A:GLU41 2.7 30.2 1.0 OE2 A:GLU41 2.8 33.3 1.0 CE1 A:HIS164 2.8 25.3 1.0 CD2 A:HIS164 3.1 25.4 1.0 O A:HOH333 3.9 36.1 1.0 ND1 A:HIS164 4.0 23.5 1.0 O A:HOH307 4.1 28.9 1.0 CG A:GLU41 4.2 31.8 1.0 CG A:HIS164 4.2 26.6 1.0 CB A:HIS163 4.3 25.0 1.0 CA A:GLU41 4.9 28.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of MTH1 in Complex with 3-Isomangostin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MTH1 in Complex with 3-Isomangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:37.9 occ:1.00 ND1 A:HIS65 2.1 28.8 1.0 SG A:CYS87 2.2 30.1 1.0 O A:HOH386 2.3 24.6 1.0 CE1 A:HIS65 2.8 33.6 1.0 CG A:HIS65 3.3 30.6 1.0 CB A:CYS87 3.4 24.1 1.0 C A:CYS87 3.6 25.2 1.0 O A:CYS87 3.6 21.7 1.0 CB A:HIS65 3.8 28.5 1.0 O A:HOH384 3.9 39.1 1.0 N A:THR88 3.9 24.9 1.0 NE2 A:HIS65 4.0 31.6 1.0 CA A:CYS87 4.0 21.7 1.0 NZ A:LYS130 4.1 39.5 1.0 CD2 A:HIS65 4.3 34.5 1.0 CA A:THR88 4.3 23.3 1.0 N A:ASP89 4.5 36.9 1.0 C A:THR88 4.5 31.5 1.0 N A:CYS87 4.7 21.4 1.0 CG1 A:VAL67 4.8 36.9 1.0 CE A:LYS130 5.0 43.7 1.0

T.Yokoyama, R.Kitakami, M.Mizuguchi. Discovery of A New Class of MTH1 Inhibitor By X-Ray Crystallographic Screening. Eur J Med Chem V. 167 153 2019.
ISSN: ISSN 1768-3254
PubMed: 30771603
DOI: 10.1016/J.EJMECH.2019.02.011