Zinc in PDB 7duz: Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7duz was solved by G.-B.Li, Y.-H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.87 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.231, 79.291, 67.267, 90, 130.28, 90
R / Rfree (%)	18 / 20.5

The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid (pdb code 7duz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid, PDB code: 7duz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-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 Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.0 occ:1.00 O A:HOH436 1.9 13.9 1.0 ND1 A:HIS116 2.0 12.2 1.0 NE2 A:HIS179 2.0 8.1 1.0 NE2 A:HIS114 2.0 7.7 1.0 CE1 A:HIS114 2.9 8.5 1.0 CD2 A:HIS179 3.0 9.8 1.0 CE1 A:HIS116 3.0 10.2 1.0 CE1 A:HIS179 3.0 10.9 1.0 CG A:HIS116 3.0 9.8 1.0 CD2 A:HIS114 3.1 8.0 1.0 CB A:HIS116 3.4 10.8 1.0 O A:HOH401 3.7 18.3 0.4 ZN A:ZN302 3.8 16.5 1.0 OD1 A:ASP118 4.0 12.9 1.0 ND1 A:HIS114 4.0 7.8 1.0 NE2 A:HIS116 4.1 14.6 1.0 ND1 A:HIS179 4.1 8.0 1.0 CG A:HIS179 4.1 6.3 1.0 CD2 A:HIS116 4.1 12.7 1.0 CG A:HIS114 4.1 6.2 1.0 O01 A:HM0304 4.2 12.4 1.0 CB A:CYS198 4.2 7.3 1.0 SG A:CYS198 4.2 13.3 1.0 OD2 A:ASP118 4.6 12.5 1.0 O A:HOH401 4.7 21.8 0.6 N04 A:HM0304 4.7 17.0 1.0 CG A:ASP118 4.7 12.9 1.0 CA A:HIS116 4.8 8.1 1.0 C02 A:HM0304 4.8 17.9 1.0 ND2 A:ASN210 4.9 30.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-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 Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.5 occ:1.00 OD2 A:ASP118 2.1 12.5 1.0 NE2 A:HIS240 2.1 10.9 1.0 O01 A:HM0304 2.2 12.4 1.0 N04 A:HM0304 2.3 17.0 1.0 O A:HOH436 2.4 13.9 1.0 SG A:CYS198 2.5 13.3 1.0 C03 A:HM0304 2.9 20.3 1.0 C02 A:HM0304 2.9 17.9 1.0 CE1 A:HIS240 3.0 11.7 1.0 CD2 A:HIS240 3.2 11.3 1.0 CG A:ASP118 3.2 12.9 1.0 C05 A:HM0304 3.4 19.5 1.0 OD1 A:ASP118 3.7 12.9 1.0 CB A:CYS198 3.7 7.3 1.0 ZN A:ZN301 3.8 13.0 1.0 NH2 A:ARG119 3.9 16.3 1.0 O12 A:HM0304 4.1 21.1 1.0 N07 A:HM0304 4.1 23.3 1.0 ND1 A:HIS240 4.2 10.7 1.0 CG A:HIS240 4.3 11.9 1.0 NE A:ARG119 4.4 11.2 1.0 O A:HOH401 4.4 18.3 0.4 C06 A:HM0304 4.4 22.1 1.0 CB A:ASP118 4.5 12.0 1.0 O A:HOH459 4.5 11.9 1.0 NE2 A:HIS179 4.5 8.1 1.0 CE1 A:HIS179 4.5 10.9 1.0 CZ A:ARG119 4.6 10.3 1.0 CE1 A:HIS114 4.7 8.5 1.0 NE2 A:HIS114 4.8 7.7 1.0 CA A:CYS198 4.9 6.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-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 Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.0 occ:1.00 O2 A:FMT306 1.9 13.5 1.0 O2 A:FMT305 2.0 14.3 1.0 ND1 A:HIS251 2.1 8.1 1.0 C A:FMT305 2.6 15.2 1.0 O1 A:FMT305 2.6 16.9 1.0 C A:FMT306 2.9 16.0 1.0 CE1 A:HIS251 3.0 9.5 1.0 CG A:HIS251 3.2 9.3 1.0 O1 A:FMT306 3.2 15.6 1.0 CB A:HIS251 3.5 7.6 1.0 CA A:HIS251 3.9 7.7 1.0 NE2 A:HIS251 4.1 8.9 1.0 CD2 A:HIS251 4.2 7.1 1.0 CD2 A:LEU203 4.4 9.4 1.0 ND2 A:ASN254 4.6 18.8 1.0 O A:HIS251 4.6 8.2 1.0 C A:HIS251 4.7 12.2 1.0 N A:HIS251 5.0 7.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-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 Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.9 occ:1.00 O B:HOH446 1.9 15.2 1.0 ND1 B:HIS116 2.0 13.1 1.0 NE2 B:HIS179 2.0 9.1 1.0 NE2 B:HIS114 2.1 7.8 1.0 CE1 B:HIS116 2.9 10.4 1.0 CE1 B:HIS114 2.9 7.0 1.0 CD2 B:HIS179 3.0 10.9 1.0 CG B:HIS116 3.0 10.9 1.0 CE1 B:HIS179 3.0 15.2 1.0 CD2 B:HIS114 3.1 10.4 1.0 CB B:HIS116 3.3 11.8 1.0 O B:HOH462 3.6 25.3 1.0 ZN B:ZN302 3.8 21.2 1.0 OD1 B:ASP118 4.0 12.6 1.0 NE2 B:HIS116 4.1 16.7 1.0 ND1 B:HIS114 4.1 7.2 1.0 ND1 B:HIS179 4.1 9.0 1.0 CD2 B:HIS116 4.1 12.9 1.0 CG B:HIS179 4.1 7.5 1.0 CG B:HIS114 4.2 7.3 1.0 SG B:CYS198 4.2 15.2 1.0 CB B:CYS198 4.2 8.1 1.0 O12 B:HM0304 4.3 15.2 1.0 OD2 B:ASP118 4.6 12.7 1.0 CG B:ASP118 4.7 13.8 1.0 ND2 B:ASN210 4.7 28.0 1.0 N04 B:HM0304 4.7 17.2 1.0 CA B:HIS116 4.8 10.3 1.0 C02 B:HM0304 4.8 22.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:21.2 occ:1.00 OD2 B:ASP118 2.1 12.7 1.0 NE2 B:HIS240 2.1 13.2 1.0 O12 B:HM0304 2.2 15.2 1.0 N04 B:HM0304 2.2 17.2 1.0 O B:HOH446 2.3 15.2 1.0 SG B:CYS198 2.5 15.2 1.0 C03 B:HM0304 2.9 23.2 1.0 C02 B:HM0304 2.9 22.1 1.0 CE1 B:HIS240 3.0 11.7 1.0 CG B:ASP118 3.2 13.8 1.0 CD2 B:HIS240 3.2 12.4 1.0 C05 B:HM0304 3.4 20.7 1.0 OD1 B:ASP118 3.6 12.6 1.0 CB B:CYS198 3.7 8.1 1.0 ZN B:ZN301 3.8 12.9 1.0 NH2 B:ARG119 4.0 17.4 1.0 N07 B:HM0304 4.1 24.1 1.0 O01 B:HM0304 4.1 21.8 1.0 ND1 B:HIS240 4.2 8.9 1.0 O B:HOH462 4.2 25.3 1.0 CG B:HIS240 4.3 11.8 1.0 NE B:ARG119 4.4 10.9 1.0 C06 B:HM0304 4.4 23.1 1.0 NE2 B:HIS179 4.4 9.1 1.0 CE1 B:HIS179 4.5 15.2 1.0 CB B:ASP118 4.5 15.8 1.0 O B:HOH452 4.6 18.0 1.0 CE1 B:HIS114 4.6 7.0 1.0 CZ B:ARG119 4.7 13.1 1.0 NE2 B:HIS114 4.8 7.8 1.0 CA B:CYS198 4.9 8.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Vim-2 Mbl in Complex with 1-Cyclobutyl-1H- Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.9 occ:1.00 O2 B:FMT305 1.9 16.9 1.0 NE2 B:HIS153 2.0 9.6 1.0 O2 B:FMT306 2.0 13.9 1.0 O1 B:FMT305 2.2 26.2 1.0 C B:FMT305 2.4 17.8 1.0 O1 B:FMT306 2.4 22.9 1.0 C B:FMT306 2.5 17.7 1.0 CE1 B:HIS153 2.9 12.8 1.0 CD2 B:HIS153 3.1 10.0 1.0 ND1 B:HIS153 4.0 11.0 1.0 CG B:HIS153 4.2 8.3 1.0 CB B:ALA132 4.2 8.4 1.0 CG2 B:THR152 4.8 9.8 1.0 CA B:ALA132 4.9 7.5 1.0

Y.H.Yan, W.Li, W.Chen, C.Li, K.R.Zhu, J.Deng, Q.Q.Dai, L.L.Yang, Z.Wang, G.B.Li. Structure-Guided Optimization of 1H-Imidazole-2-Carboxylic Acid Derivatives Affording Potent Vim-Type Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 228 13965 2022.
ISSN: ISSN 0223-5234
PubMed: 34763944
DOI: 10.1016/J.EJMECH.2021.113965