Zinc in PDB 3vw9: Human Glyoxalase I with An N-Hydroxypyridone Inhibitor

All present enzymatic activity of Human Glyoxalase I with An N-Hydroxypyridone Inhibitor:
4.4.1.5;

The structure of Human Glyoxalase I with An N-Hydroxypyridone Inhibitor, PDB code: 3vw9 was solved by T.A.Fukami, M.Irie, T.Matsuura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.52 / 1.47
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.990, 66.980, 68.530, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.3

The binding sites of Zinc atom in the Human Glyoxalase I with An N-Hydroxypyridone Inhibitor (pdb code 3vw9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Glyoxalase I with An N-Hydroxypyridone Inhibitor, PDB code: 3vw9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Glyoxalase I with An N-Hydroxypyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glyoxalase I with An N-Hydroxypyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.9 occ:1.00 OE1 A:GLU99 2.0 22.0 1.0 OE1 A:GLN33 2.0 17.0 1.0 NE2 B:HIS126 2.2 11.7 1.0 O21 B:HPJ202 2.2 17.3 1.0 OE1 B:GLU172 2.3 18.9 1.0 O18 B:HPJ202 2.3 23.3 1.0 CD A:GLU99 2.8 34.7 1.0 CD A:GLN33 3.0 19.1 1.0 OE2 A:GLU99 3.1 34.0 1.0 C20 B:HPJ202 3.1 15.8 1.0 N17 B:HPJ202 3.2 16.3 1.0 CE1 B:HIS126 3.2 12.0 1.0 CD2 B:HIS126 3.2 12.1 1.0 CD B:GLU172 3.3 25.5 1.0 NE2 A:GLN33 3.5 13.7 1.0 OE2 B:GLU172 3.7 25.9 1.0 CG A:GLU99 4.3 15.7 1.0 CG A:GLN33 4.3 13.2 1.0 ND1 B:HIS126 4.3 11.8 1.0 CG B:HIS126 4.4 10.5 1.0 C22 B:HPJ202 4.4 16.5 1.0 O A:HOH334 4.5 19.1 1.0 CB A:MET35 4.5 10.6 1.0 C15 B:HPJ202 4.5 15.5 1.0 CG B:GLU172 4.6 12.1 1.0 CB B:GLU172 4.7 9.1 1.0 CG A:MET35 4.7 12.0 1.0 CB A:GLU99 4.7 10.6 1.0 C13 B:HPJ202 5.0 18.6 1.0

Zinc binding site 2 out of 2 in the Human Glyoxalase I with An N-Hydroxypyridone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glyoxalase I with An N-Hydroxypyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:20.4 occ:1.00 OE1 B:GLN33 2.0 15.5 1.0 OE1 B:GLU99 2.1 17.8 1.0 NE2 A:HIS126 2.2 12.2 1.0 O21 A:HPJ203 2.2 15.5 1.0 OE1 A:GLU172 2.3 18.6 1.0 O18 A:HPJ203 2.3 26.0 1.0 CD B:GLU99 2.9 24.0 1.0 CD B:GLN33 3.0 16.5 1.0 OE2 B:GLU99 3.1 24.5 1.0 C20 A:HPJ203 3.1 15.4 1.0 CE1 A:HIS126 3.1 12.2 1.0 N17 A:HPJ203 3.2 14.9 1.0 CD2 A:HIS126 3.2 12.4 1.0 CD A:GLU172 3.3 29.0 1.0 NE2 B:GLN33 3.5 11.2 1.0 OE2 A:GLU172 3.6 30.5 1.0 ND1 A:HIS126 4.3 11.8 1.0 CG B:GLU99 4.3 12.5 1.0 CG A:HIS126 4.3 11.6 1.0 CG B:GLN33 4.4 11.8 1.0 O B:HOH1021 4.4 15.7 1.0 C22 A:HPJ203 4.4 13.6 1.0 C15 A:HPJ203 4.5 13.3 1.0 CB B:MET35 4.5 7.9 1.0 CG A:GLU172 4.6 13.6 1.0 CB A:GLU172 4.7 8.5 1.0 CG B:MET35 4.7 9.8 1.0 CB B:GLU99 4.8 8.4 1.0 C13 A:HPJ203 4.9 15.0 1.0

T.Chiba, J.Ohwada, H.Sakamoto, T.Kobayashi, T.A.Fukami, M.Irie, T.Miura, K.Ohara, H.Koyano. Design and Evaluation of Azaindole-Substituted N-Hydroxypyridones As Glyoxalase I Inhibitors Bioorg.Med.Chem.Lett. V. 22 7486 2012.
ISSN: ISSN 0960-894X
PubMed: 23122816
DOI: 10.1016/J.BMCL.2012.10.045