Zinc in PDB 8hxu: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-4-Carboxylic Acid, PDB code: 8hxu 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)	19.92 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.078, 90.448, 126.573, 90, 90, 90
R / Rfree (%)	19.5 / 24.1

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-4-Carboxylic Acid (pdb code 8hxu). 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- Pentylthiazole-4-Carboxylic Acid, PDB code: 8hxu:
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- Pentylthiazole-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- Pentylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:42.5 occ:1.00 ND1 A:HIS116 1.9 32.4 1.0 NE2 A:HIS179 2.0 43.9 1.0 NE2 A:HIS114 2.1 33.8 1.0 O A:HOH405 2.5 42.0 1.0 CE1 A:HIS116 2.8 43.0 1.0 CE1 A:HIS114 3.0 37.0 1.0 CD2 A:HIS179 3.0 39.1 1.0 CE1 A:HIS179 3.0 41.9 1.0 CG A:HIS116 3.0 38.9 1.0 CD2 A:HIS114 3.2 34.5 1.0 CB A:HIS116 3.5 38.5 1.0 ZN A:ZN302 3.8 42.4 1.0 OD1 A:ASP118 3.9 31.7 1.0 NE2 A:HIS116 4.0 36.9 1.0 CD2 A:HIS116 4.1 34.7 1.0 ND1 A:HIS179 4.1 44.3 1.0 ND1 A:HIS114 4.1 41.6 1.0 CG A:HIS179 4.1 39.5 1.0 SG A:CYS198 4.1 38.5 1.0 O07 A:5Z2303 4.2 47.6 1.0 CG A:HIS114 4.3 38.4 1.0 CB A:CYS198 4.3 38.8 1.0 OD2 A:ASP118 4.5 33.5 1.0 CG A:ASP118 4.7 34.4 1.0 N03 A:5Z2303 4.8 37.2 1.0 C05 A:5Z2303 4.9 46.4 1.0 CA A:HIS116 4.9 43.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-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- Pentylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:42.4 occ:1.00 O A:HOH405 1.7 42.0 1.0 NE2 A:HIS240 2.1 35.5 1.0 O07 A:5Z2303 2.1 47.6 1.0 OD2 A:ASP118 2.2 33.5 1.0 N03 A:5Z2303 2.3 37.2 1.0 SG A:CYS198 2.5 38.5 1.0 C05 A:5Z2303 2.9 46.4 1.0 CE1 A:HIS240 2.9 35.1 1.0 C04 A:5Z2303 3.0 42.9 1.0 CD2 A:HIS240 3.2 41.4 1.0 CG A:ASP118 3.3 34.4 1.0 C02 A:5Z2303 3.4 42.5 1.0 CB A:CYS198 3.7 38.8 1.0 OD1 A:ASP118 3.7 31.7 1.0 ZN A:ZN301 3.8 42.5 1.0 N01 A:5Z2303 3.9 41.5 1.0 NH2 A:ARG119 4.0 42.7 1.0 ND1 A:HIS240 4.1 31.8 1.0 O06 A:5Z2303 4.1 48.9 1.0 CG A:HIS240 4.2 39.4 1.0 C08 A:5Z2303 4.3 52.5 1.0 CE1 A:HIS179 4.4 41.9 1.0 O A:HOH440 4.4 42.5 1.0 NE2 A:HIS179 4.5 43.9 1.0 CB A:ASP118 4.6 33.0 1.0 NE A:ARG119 4.6 35.4 1.0 S14 A:5Z2303 4.7 44.4 1.0 CE1 A:HIS114 4.7 37.0 1.0 CZ A:ARG119 4.8 33.4 1.0 NE2 A:HIS114 4.9 33.8 1.0 CA A:CYS198 4.9 44.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-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- Pentylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:42.4 occ:1.00 NE2 B:HIS179 2.0 46.0 1.0 ND1 B:HIS116 2.0 41.2 1.0 O B:HOH437 2.0 44.5 1.0 NE2 B:HIS114 2.1 40.5 1.0 CE1 B:HIS116 2.9 44.7 1.0 CE1 B:HIS114 2.9 37.7 1.0 CD2 B:HIS179 2.9 34.2 1.0 CE1 B:HIS179 3.0 44.5 1.0 CG B:HIS116 3.0 46.0 1.0 CD2 B:HIS114 3.1 44.0 1.0 CB B:HIS116 3.4 39.7 1.0 O B:HOH492 3.6 45.2 1.0 ZN B:ZN302 3.7 45.6 1.0 OD1 B:ASP118 3.9 40.6 1.0 NE2 B:HIS116 4.0 43.5 1.0 ND1 B:HIS114 4.0 36.1 1.0 ND1 B:HIS179 4.0 42.4 1.0 CG B:HIS179 4.1 42.9 1.0 CD2 B:HIS116 4.1 43.2 1.0 SG B:CYS198 4.1 41.8 1.0 CG B:HIS114 4.2 38.9 1.0 CB B:CYS198 4.2 40.5 1.0 O07 B:5Z2303 4.4 41.1 1.0 OD2 B:ASP118 4.6 34.0 1.0 CG B:ASP118 4.7 39.0 1.0 CA B:HIS116 4.8 38.9 1.0 N03 B:5Z2303 4.8 47.8 1.0 C05 B:5Z2303 4.9 49.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Pentylthiazole-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- Pentylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:45.6 occ:1.00 OD2 B:ASP118 2.2 34.0 1.0 NE2 B:HIS240 2.2 43.1 1.0 O07 B:5Z2303 2.3 41.1 1.0 N03 B:5Z2303 2.3 47.8 1.0 SG B:CYS198 2.4 41.8 1.0 O B:HOH437 2.4 44.5 1.0 C05 B:5Z2303 3.0 49.8 1.0 C04 B:5Z2303 3.0 47.8 1.0 CE1 B:HIS240 3.1 41.9 1.0 CD2 B:HIS240 3.2 40.8 1.0 CG B:ASP118 3.2 39.0 1.0 C02 B:5Z2303 3.3 45.4 1.0 CB B:CYS198 3.6 40.5 1.0 OD1 B:ASP118 3.6 40.6 1.0 N01 B:5Z2303 3.7 43.0 1.0 ZN B:ZN301 3.7 42.4 1.0 O B:HOH492 4.2 45.2 1.0 ND1 B:HIS240 4.2 41.6 1.0 O06 B:5Z2303 4.2 52.0 1.0 NH2 B:ARG119 4.2 39.4 1.0 CG B:HIS240 4.3 44.1 1.0 NE2 B:HIS179 4.4 46.0 1.0 CE1 B:HIS179 4.4 44.5 1.0 C08 B:5Z2303 4.4 50.7 1.0 O B:HOH433 4.5 43.9 1.0 CB B:ASP118 4.6 31.8 1.0 NE B:ARG119 4.6 33.1 1.0 CE1 B:HIS114 4.7 37.7 1.0 S14 B:5Z2303 4.7 49.9 1.0 NE2 B:HIS114 4.8 40.5 1.0 CA B:CYS198 4.9 45.7 1.0 CZ B:ARG119 4.9 40.1 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