Zinc in PDB 8hy1: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid, PDB code: 8hy1 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)	27.04 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.561, 89.724, 126.565, 90, 90, 90
R / Rfree (%)	18.6 / 22.4

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid (pdb code 8hy1). 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-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid, PDB code: 8hy1:
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-(Thiophen- 2-Ylmethyl)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-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.4 occ:1.00 NE2 A:HIS179 2.0 15.3 1.0 ND1 A:HIS116 2.0 19.5 1.0 O A:HOH412 2.0 12.7 1.0 NE2 A:HIS114 2.0 15.7 1.0 CE1 A:HIS114 2.9 17.4 1.0 CD2 A:HIS179 3.0 16.2 1.0 CE1 A:HIS116 3.0 17.7 1.0 CE1 A:HIS179 3.0 16.6 1.0 CG A:HIS116 3.0 19.0 1.0 CD2 A:HIS114 3.1 15.4 1.0 CB A:HIS116 3.4 14.5 1.0 ZN A:ZN302 3.6 18.3 1.0 OD1 A:ASP118 3.8 14.1 1.0 SG A:CYS198 3.9 17.4 1.0 CB A:CYS198 3.9 14.2 1.0 ND1 A:HIS114 4.0 13.4 1.0 ND1 A:HIS179 4.1 17.2 1.0 NE2 A:HIS116 4.1 21.1 1.0 CG A:HIS179 4.1 15.4 1.0 CD2 A:HIS116 4.1 20.1 1.0 CG A:HIS114 4.2 13.9 1.0 O03 A:5ZU303 4.2 16.7 1.0 OD2 A:ASP118 4.5 8.8 1.0 CG A:ASP118 4.6 16.2 1.0 CA A:HIS116 4.8 14.5 1.0 N15 A:5ZU303 4.8 15.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)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-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.3 occ:1.00 O A:HOH412 2.1 12.7 1.0 OD2 A:ASP118 2.1 8.8 1.0 NE2 A:HIS240 2.2 11.5 1.0 N15 A:5ZU303 2.3 15.7 1.0 O03 A:5ZU303 2.3 16.7 1.0 SG A:CYS198 2.4 17.4 1.0 C04 A:5ZU303 3.1 17.9 1.0 C02 A:5ZU303 3.1 21.3 1.0 CE1 A:HIS240 3.1 15.5 1.0 CD2 A:HIS240 3.2 14.7 1.0 CG A:ASP118 3.2 16.2 1.0 C13 A:5ZU303 3.3 19.4 1.0 OD1 A:ASP118 3.5 14.1 1.0 ZN A:ZN301 3.6 16.4 1.0 CB A:CYS198 3.7 14.2 1.0 N14 A:5ZU303 3.7 20.1 1.0 NH2 A:ARG119 4.1 16.2 1.0 ND1 A:HIS240 4.2 14.6 1.0 O01 A:5ZU303 4.3 20.8 1.0 CG A:HIS240 4.3 13.2 1.0 NE2 A:HIS179 4.3 15.3 1.0 CE1 A:HIS179 4.3 16.6 1.0 C05 A:5ZU303 4.4 24.9 1.0 CB A:ASP118 4.5 11.5 1.0 O A:HOH459 4.5 16.0 1.0 NE A:ARG119 4.5 13.6 1.0 S12 A:5ZU303 4.7 22.4 1.0 CE1 A:HIS114 4.7 17.4 1.0 NE2 A:HIS114 4.8 15.7 1.0 CA A:CYS198 4.8 14.8 1.0 CZ A:ARG119 4.8 16.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)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-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.3 occ:1.00 ND1 B:HIS116 1.9 15.2 1.0 NE2 B:HIS179 2.0 19.6 1.0 NE2 B:HIS114 2.1 14.4 1.0 O B:HOH411 2.2 11.2 1.0 CE1 B:HIS116 2.8 19.9 1.0 CE1 B:HIS114 2.9 13.0 1.0 CD2 B:HIS179 3.0 13.4 1.0 CE1 B:HIS179 3.0 18.5 1.0 CG B:HIS116 3.1 13.3 1.0 CD2 B:HIS114 3.2 15.1 1.0 CB B:HIS116 3.5 8.2 1.0 ZN B:ZN302 3.6 17.4 1.0 OD1 B:ASP118 3.8 14.5 1.0 NE2 B:HIS116 4.0 20.2 1.0 SG B:CYS198 4.0 13.4 1.0 ND1 B:HIS114 4.0 18.2 1.0 CB B:CYS198 4.1 10.0 1.0 CD2 B:HIS116 4.1 14.5 1.0 ND1 B:HIS179 4.1 19.1 1.0 CG B:HIS179 4.1 15.2 1.0 CG B:HIS114 4.2 14.9 1.0 ND2 B:ASN210 4.3 36.1 1.0 O03 B:5ZU303 4.3 21.0 1.0 OD2 B:ASP118 4.5 10.8 1.0 CG B:ASP118 4.6 14.2 1.0 N15 B:5ZU303 4.9 14.0 1.0 CA B:HIS116 4.9 17.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(Thiophen- 2-Ylmethyl)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-(Thiophen- 2-Ylmethyl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.4 occ:1.00 O B:HOH411 1.9 11.2 1.0 NE2 B:HIS240 2.1 11.3 1.0 OD2 B:ASP118 2.2 10.8 1.0 O03 B:5ZU303 2.2 21.0 1.0 N15 B:5ZU303 2.3 14.0 1.0 SG B:CYS198 2.5 13.4 1.0 C04 B:5ZU303 3.0 16.8 1.0 C02 B:5ZU303 3.0 18.4 1.0 CE1 B:HIS240 3.0 12.3 1.0 CD2 B:HIS240 3.2 14.0 1.0 CG B:ASP118 3.2 14.2 1.0 C13 B:5ZU303 3.3 19.4 1.0 ZN B:ZN301 3.6 16.3 1.0 OD1 B:ASP118 3.6 14.5 1.0 CB B:CYS198 3.6 10.0 1.0 N14 B:5ZU303 3.8 17.6 1.0 NH2 B:ARG119 4.0 16.4 1.0 ND1 B:HIS240 4.2 11.6 1.0 O01 B:5ZU303 4.2 19.8 1.0 NE2 B:HIS179 4.2 19.6 1.0 CG B:HIS240 4.3 10.2 1.0 CE1 B:HIS179 4.3 18.5 1.0 C05 B:5ZU303 4.3 20.6 1.0 O B:HOH451 4.5 17.5 1.0 NE B:ARG119 4.5 10.2 1.0 CB B:ASP118 4.5 8.0 1.0 ND2 B:ASN210 4.6 36.1 1.0 S12 B:5ZU303 4.7 20.0 1.0 CE1 B:HIS114 4.7 13.0 1.0 CZ B:ARG119 4.8 12.4 1.0 CA B:CYS198 4.8 14.6 1.0 NE2 B:HIS114 4.8 14.4 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