Zinc in PDB 8hyd: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid, PDB code: 8hyd 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)	19.55 / 1.71
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.009, 64.533, 90.678, 90, 90, 90
R / Rfree (%)	16.6 / 20.1

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

Zinc binding site 1 out of 2 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)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-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:29.1 occ:1.00 ND1 A:HIS116 1.9 24.1 1.0 NE2 A:HIS179 2.0 27.0 1.0 O A:HOH440 2.1 27.2 1.0 NE2 A:HIS114 2.1 26.3 1.0 CE1 A:HIS116 2.8 33.4 1.0 CD2 A:HIS179 3.0 30.7 1.0 CG A:HIS116 3.0 25.8 1.0 CE1 A:HIS179 3.0 33.8 1.0 CD2 A:HIS114 3.0 23.7 1.0 CE1 A:HIS114 3.1 25.3 1.0 CB A:HIS116 3.4 22.8 1.0 ZN A:ZN302 3.6 37.4 1.0 O A:HOH500 3.8 45.6 1.0 OD1 A:ASP118 3.9 28.0 1.0 NE2 A:HIS116 3.9 30.4 1.0 CD2 A:HIS116 4.0 32.6 1.0 SG A:CYS198 4.1 31.0 1.0 ND1 A:HIS179 4.1 33.1 1.0 CG A:HIS179 4.1 28.0 1.0 ND1 A:HIS114 4.1 27.0 1.0 CG A:HIS114 4.2 21.2 1.0 CB A:CYS198 4.2 34.3 1.0 O06 A:60J303 4.2 37.3 1.0 OD2 A:ASP118 4.5 23.5 1.0 CG A:ASP118 4.6 29.3 1.0 CA A:HIS116 4.8 23.9 1.0 N03 A:60J303 4.9 34.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)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-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:37.4 occ:1.00 O A:HOH440 2.1 27.2 1.0 OD2 A:ASP118 2.1 23.5 1.0 NE2 A:HIS240 2.2 30.0 1.0 O06 A:60J303 2.2 37.3 1.0 N03 A:60J303 2.4 34.8 1.0 SG A:CYS198 2.7 31.0 1.0 C05 A:60J303 3.0 45.7 1.0 C04 A:60J303 3.0 43.8 1.0 CE1 A:HIS240 3.1 32.7 1.0 CG A:ASP118 3.2 29.3 1.0 CD2 A:HIS240 3.3 32.2 1.0 C02 A:60J303 3.4 43.9 1.0 O A:HOH475 3.5 47.1 1.0 ZN A:ZN301 3.6 29.1 1.0 OD1 A:ASP118 3.6 28.0 1.0 N01 A:60J303 3.8 37.8 1.0 CB A:CYS198 4.0 34.3 1.0 O07 A:60J303 4.2 43.4 1.0 NH2 A:ARG119 4.2 30.2 1.0 ND1 A:HIS240 4.3 27.0 1.0 C08 A:60J303 4.3 48.9 1.0 NE2 A:HIS179 4.3 27.0 1.0 CE1 A:HIS179 4.3 33.8 1.0 CG A:HIS240 4.4 30.4 1.0 CB A:ASP118 4.4 23.8 1.0 O A:HOH500 4.5 45.6 1.0 NE A:ARG119 4.6 21.7 1.0 S16 A:60J303 4.6 42.6 1.0 O A:HOH441 4.7 36.4 1.0 NE2 A:HIS114 4.7 26.3 1.0 CE1 A:HIS114 4.8 25.3 1.0 O A:HOH430 4.8 41.5 1.0 CZ A:ARG119 4.9 29.5 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