Zinc in PDB 8hx5: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hx5 was solved by Y.-H.Yan, K.-R.Zhu, G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.742, 91.045, 125.69, 90, 90, 90
R / Rfree (%)	19.8 / 28.6

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid (pdb code 8hx5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hx5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid


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 B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:42.3 occ:1.00 ND1 A:HIS116 2.0 38.0 1.0 NE2 A:HIS114 2.0 33.8 1.0 NE2 A:HIS179 2.0 48.7 1.0 O A:HOH401 2.4 46.8 1.0 CE1 A:HIS179 2.6 39.8 1.0 CE1 A:HIS114 2.6 31.8 1.0 CE1 A:HIS116 2.8 40.6 1.0 CG A:HIS116 3.1 43.3 1.0 CD2 A:HIS114 3.2 41.7 1.0 CD2 A:HIS179 3.3 37.5 1.0 CB A:HIS116 3.5 41.5 1.0 ZN A:ZN302 3.6 48.6 1.0 ND1 A:HIS179 3.8 37.0 1.0 ND1 A:HIS114 3.8 33.7 1.0 OD1 A:ASP118 3.8 37.6 1.0 SG A:CYS198 3.9 35.1 1.0 CB A:CYS198 4.0 41.0 1.0 NE2 A:HIS116 4.0 37.7 1.0 CG A:HIS114 4.1 37.1 1.0 CD2 A:HIS116 4.1 39.8 1.0 CG A:HIS179 4.2 35.2 1.0 OD2 A:ASP118 4.3 33.3 1.0 O06 A:4YJ303 4.4 47.1 1.0 CG A:ASP118 4.5 45.6 1.0 N03 A:4YJ303 4.9 35.9 1.0 CA A:HIS116 4.9 42.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid


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 B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:48.6 occ:1.00 O A:HOH401 1.6 46.8 1.0 OD2 A:ASP118 2.1 33.3 1.0 NE2 A:HIS240 2.1 43.1 1.0 N03 A:4YJ303 2.3 35.9 1.0 SG A:CYS198 2.4 35.1 1.0 O06 A:4YJ303 2.4 47.1 1.0 CE1 A:HIS240 2.8 46.3 1.0 C04 A:4YJ303 3.1 43.2 1.0 C05 A:4YJ303 3.1 47.6 1.0 CG A:ASP118 3.2 45.6 1.0 CD2 A:HIS240 3.3 40.9 1.0 C02 A:4YJ303 3.3 40.9 1.0 CB A:CYS198 3.4 41.0 1.0 ZN A:ZN301 3.6 42.3 1.0 N01 A:4YJ303 3.7 38.6 1.0 OD1 A:ASP118 3.8 37.6 1.0 NH2 A:ARG119 3.9 36.2 1.0 ND1 A:HIS240 4.0 39.2 1.0 CG A:HIS240 4.3 41.2 1.0 CE1 A:HIS179 4.3 39.8 1.0 O07 A:4YJ303 4.4 54.1 1.0 NE A:ARG119 4.4 39.1 1.0 C08 A:4YJ303 4.5 48.0 1.0 CB A:ASP118 4.5 34.9 1.0 NE2 A:HIS179 4.5 48.7 1.0 CE1 A:HIS114 4.6 31.8 1.0 CA A:CYS198 4.6 42.4 1.0 CZ A:ARG119 4.6 36.5 1.0 S18 A:4YJ303 4.8 60.0 1.0 NE2 A:HIS114 4.9 33.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid


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 B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:38.3 occ:1.00 ND1 B:HIS116 2.0 27.8 1.0 NE2 B:HIS179 2.0 29.1 1.0 NE2 B:HIS114 2.1 33.0 1.0 O B:HOH403 2.3 33.7 1.0 CE1 B:HIS114 2.7 32.5 1.0 CD2 B:HIS179 2.9 32.1 1.0 CE1 B:HIS116 3.0 34.5 1.0 CG B:HIS116 3.0 30.1 1.0 CE1 B:HIS179 3.0 38.7 1.0 CD2 B:HIS114 3.3 38.1 1.0 CB B:HIS116 3.3 33.9 1.0 ZN B:ZN302 3.6 41.8 1.0 SG B:CYS198 3.8 34.6 1.0 ND1 B:HIS114 3.9 33.1 1.0 OD1 B:ASP118 4.0 27.2 1.0 CB B:CYS198 4.1 43.3 1.0 CG B:HIS179 4.1 30.0 1.0 ND1 B:HIS179 4.1 35.5 1.0 NE2 B:HIS116 4.1 36.6 1.0 CD2 B:HIS116 4.1 32.7 1.0 O06 B:4YJ303 4.2 38.3 1.0 CG B:HIS114 4.2 35.9 1.0 OD2 B:ASP118 4.5 31.2 1.0 CG B:ASP118 4.7 30.3 1.0 CA B:HIS116 4.8 38.6 1.0 N03 B:4YJ303 4.8 38.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(4- Methoxybenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:41.8 occ:1.00 O B:HOH403 1.8 33.7 1.0 NE2 B:HIS240 2.2 40.6 1.0 OD2 B:ASP118 2.2 31.2 1.0 O06 B:4YJ303 2.3 38.3 1.0 SG B:CYS198 2.4 34.6 1.0 N03 B:4YJ303 2.4 38.0 1.0 CE1 B:HIS240 2.9 41.2 1.0 C05 B:4YJ303 3.1 37.7 1.0 C04 B:4YJ303 3.2 38.5 1.0 CG B:ASP118 3.3 30.3 1.0 C02 B:4YJ303 3.4 32.7 1.0 CD2 B:HIS240 3.4 33.6 1.0 ZN B:ZN301 3.6 38.3 1.0 CB B:CYS198 3.6 43.3 1.0 N01 B:4YJ303 3.7 30.2 1.0 NH2 B:ARG119 3.7 35.9 1.0 OD1 B:ASP118 3.7 27.2 1.0 ND1 B:HIS240 4.1 41.2 1.0 O07 B:4YJ303 4.3 46.4 1.0 CE1 B:HIS179 4.4 38.7 1.0 NE2 B:HIS179 4.4 29.1 1.0 CG B:HIS240 4.4 36.6 1.0 C08 B:4YJ303 4.5 44.0 1.0 NE B:ARG119 4.5 28.3 1.0 CZ B:ARG119 4.6 28.4 1.0 CB B:ASP118 4.6 31.1 1.0 CE1 B:HIS114 4.7 32.5 1.0 S18 B:4YJ303 4.8 45.7 1.0 CA B:CYS198 4.8 42.5 1.0 NE2 B:HIS114 4.9 33.0 1.0

Y.H.Yan, T.T.Zhang, R.Li, S.Y.Wang, L.L.Wei, X.Y.Wang, K.R.Zhu, S.R.Li, G.Q.Liang, Z.B.Yang, L.L.Yang, S.Qin, G.B.Li. Discovery of 2-Aminothiazole-4-Carboxylic Acids As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors By Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. V. 66 13746 2023.
ISSN: ISSN 0022-2623
PubMed: 37791640
DOI: 10.1021/ACS.JMEDCHEM.3C01189