Zinc in PDB 8hxp: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 8hxp 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)	19.75 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.958, 90.202, 125.082, 90, 90, 90
R / Rfree (%)	17.3 / 21.6

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid (pdb code 8hxp). 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-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 8hxp:
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-(But-3-En- 1-Yl)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-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:30.2 occ:1.00 O A:HOH474 1.9 27.4 1.0 NE2 A:HIS179 2.0 30.9 1.0 NE2 A:HIS114 2.0 27.8 1.0 ND1 A:HIS116 2.0 32.3 1.0 CE1 A:HIS114 2.8 24.5 1.0 CD2 A:HIS179 2.9 29.4 1.0 CE1 A:HIS116 3.0 29.8 1.0 CG A:HIS116 3.0 32.6 1.0 CE1 A:HIS179 3.1 30.1 1.0 CD2 A:HIS114 3.1 25.6 1.0 CB A:HIS116 3.4 25.6 1.0 ZN A:ZN302 3.7 29.1 1.0 OD1 A:ASP118 3.9 26.6 1.0 ND1 A:HIS114 4.0 25.3 1.0 SG A:CYS198 4.1 25.4 1.0 CG A:HIS179 4.1 29.6 1.0 NE2 A:HIS116 4.1 30.8 1.0 CB A:CYS198 4.1 26.5 1.0 ND1 A:HIS179 4.1 33.0 1.0 CD2 A:HIS116 4.1 26.7 1.0 CG A:HIS114 4.2 24.2 1.0 ND2 A:ASN210 4.2 50.3 1.0 O07 A:5YT303 4.3 27.6 1.0 OD2 A:ASP118 4.6 21.7 1.0 N03 A:5YT303 4.7 39.6 1.0 CG A:ASP118 4.7 22.1 1.0 CA A:HIS116 4.8 26.0 1.0 C05 A:5YT303 5.0 38.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)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-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.1 occ:1.00 NE2 A:HIS240 2.1 28.3 1.0 OD2 A:ASP118 2.1 21.7 1.0 O A:HOH474 2.2 27.4 1.0 N03 A:5YT303 2.2 39.6 1.0 O07 A:5YT303 2.2 27.6 1.0 SG A:CYS198 2.4 25.4 1.0 C04 A:5YT303 3.0 43.7 1.0 CE1 A:HIS240 3.0 30.2 1.0 C05 A:5YT303 3.0 38.5 1.0 CG A:ASP118 3.2 22.1 1.0 CD2 A:HIS240 3.2 30.5 1.0 C02 A:5YT303 3.3 45.3 1.0 OD1 A:ASP118 3.6 26.6 1.0 CB A:CYS198 3.6 26.5 1.0 N01 A:5YT303 3.7 38.5 1.0 ZN A:ZN301 3.7 30.2 1.0 NH2 A:ARG119 4.1 24.1 1.0 ND1 A:HIS240 4.1 28.7 1.0 O06 A:5YT303 4.2 35.3 1.0 NE2 A:HIS179 4.2 30.9 1.0 CG A:HIS240 4.3 26.8 1.0 C08 A:5YT303 4.3 58.6 1.0 CE1 A:HIS179 4.3 30.1 1.0 O A:HOH436 4.4 28.4 1.0 CB A:ASP118 4.5 21.9 1.0 NE A:ARG119 4.5 20.0 1.0 CE1 A:HIS114 4.6 24.5 1.0 S13 A:5YT303 4.6 55.0 1.0 ND2 A:ASN210 4.7 50.3 1.0 CA A:CYS198 4.7 27.7 1.0 NE2 A:HIS114 4.8 27.8 1.0 CZ A:ARG119 4.8 27.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)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-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:27.9 occ:1.00 ND1 B:HIS116 1.9 24.6 1.0 NE2 B:HIS179 2.0 29.0 1.0 NE2 B:HIS114 2.1 27.0 1.0 O B:HOH420 2.2 23.4 1.0 CE1 B:HIS116 2.8 23.9 1.0 CE1 B:HIS114 2.9 21.6 1.0 CD2 B:HIS179 2.9 24.9 1.0 CG B:HIS116 3.0 22.2 1.0 CE1 B:HIS179 3.0 23.6 1.0 CD2 B:HIS114 3.2 24.9 1.0 CB B:HIS116 3.4 20.5 1.0 O B:HOH410 3.8 37.0 1.0 ZN B:ZN302 3.8 27.5 1.0 OD1 B:ASP118 3.9 19.6 1.0 NE2 B:HIS116 3.9 28.7 1.0 ND1 B:HIS114 4.0 26.2 1.0 CD2 B:HIS116 4.0 26.8 1.0 CG B:HIS179 4.0 21.7 1.0 SG B:CYS198 4.1 23.4 1.0 ND1 B:HIS179 4.1 27.3 1.0 CG B:HIS114 4.2 24.9 1.0 CB B:CYS198 4.2 21.4 1.0 O07 B:5YT303 4.3 25.2 1.0 OD2 B:ASP118 4.6 22.8 1.0 N03 B:5YT303 4.6 35.2 1.0 CG B:ASP118 4.7 24.9 1.0 CA B:HIS116 4.8 28.0 1.0 ND2 B:ASN210 4.9 47.7 1.0 C05 B:5YT303 4.9 34.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5-(But-3-En- 1-Yl)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-(But-3-En- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.5 occ:1.00 O B:HOH420 1.9 23.4 1.0 OD2 B:ASP118 2.1 22.8 1.0 NE2 B:HIS240 2.1 20.2 1.0 N03 B:5YT303 2.2 35.2 1.0 O07 B:5YT303 2.3 25.2 1.0 SG B:CYS198 2.4 23.4 1.0 C04 B:5YT303 2.9 34.0 1.0 C05 B:5YT303 2.9 34.8 1.0 CE1 B:HIS240 2.9 22.2 1.0 CG B:ASP118 3.2 24.9 1.0 CD2 B:HIS240 3.2 22.5 1.0 C02 B:5YT303 3.3 41.8 1.0 OD1 B:ASP118 3.6 19.6 1.0 CB B:CYS198 3.7 21.4 1.0 N01 B:5YT303 3.8 40.5 1.0 ZN B:ZN301 3.8 27.9 1.0 NH2 B:ARG119 3.9 27.0 1.0 ND1 B:HIS240 4.1 19.4 1.0 O06 B:5YT303 4.1 31.4 1.0 C08 B:5YT303 4.2 52.7 1.0 NE2 B:HIS179 4.3 29.0 1.0 CG B:HIS240 4.3 21.1 1.0 CE1 B:HIS179 4.3 23.6 1.0 O B:HOH410 4.4 37.0 1.0 CB B:ASP118 4.5 20.8 1.0 O B:HOH454 4.5 29.3 1.0 NE B:ARG119 4.6 23.6 1.0 S13 B:5YT303 4.6 47.7 1.0 CE1 B:HIS114 4.7 21.6 1.0 CZ B:ARG119 4.7 18.4 1.0 CA B:CYS198 4.8 23.4 1.0 NE2 B:HIS114 4.9 27.0 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