Fluorine in PDB 7dv0: Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dv0 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)	28.96 / 1.60
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.148, 64.535, 90.995, 90, 90, 90
R / Rfree (%)	18.1 / 21.2

The structure of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid (pdb code 7dv0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid, PDB code: 7dv0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:25.3 occ:1.00 F17 A:HML303 0.0 25.3 1.0 C16 A:HML303 1.4 22.1 1.0 F18 A:HML303 2.2 23.9 1.0 F19 A:HML303 2.2 28.9 1.0 C13 A:HML303 2.4 18.0 1.0 C12 A:HML303 3.1 15.5 1.0 O A:HOH457 3.1 16.2 1.0 OE2 A:GLU202 3.2 21.0 1.0 C14 A:HML303 3.3 16.0 1.0 CD A:ARG205 3.6 18.6 1.0 O A:HOH435 3.7 23.8 1.0 O A:HIS240 3.8 14.6 1.0 CG A:GLU202 3.8 15.7 1.0 CD A:GLU202 3.9 16.8 1.0 CB A:HIS240 4.0 10.7 1.0 NH1 A:ARG205 4.1 17.2 1.0 CB A:ARG205 4.2 19.7 1.0 CG A:ARG205 4.2 22.4 1.0 NE A:ARG205 4.3 19.1 1.0 C A:HIS240 4.3 12.9 1.0 C11 A:HML303 4.4 18.3 1.0 O A:HOH484 4.5 17.2 1.0 C15 A:HML303 4.5 15.0 1.0 CZ A:ARG205 4.6 19.1 1.0 CA A:HIS240 4.8 11.8 1.0 C10 A:HML303 5.0 16.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:23.9 occ:1.00 F18 A:HML303 0.0 23.9 1.0 C16 A:HML303 1.4 22.1 1.0 F17 A:HML303 2.2 25.3 1.0 F19 A:HML303 2.2 28.9 1.0 C13 A:HML303 2.4 18.0 1.0 C14 A:HML303 2.8 16.0 1.0 CD A:PRO68 3.3 9.1 1.0 CG A:PRO68 3.5 8.8 1.0 O A:HOH484 3.5 17.2 1.0 CB A:HIS240 3.6 10.7 1.0 C12 A:HML303 3.7 15.5 1.0 OE2 A:GLU202 3.7 21.0 1.0 C15 A:HML303 4.1 15.0 1.0 O A:PRO68 4.3 10.0 1.0 C A:HIS240 4.3 12.9 1.0 CD1 A:TYR67 4.3 14.3 1.0 O A:HIS240 4.4 14.6 1.0 N A:PRO68 4.5 8.3 1.0 N A:GLY241 4.5 11.5 1.0 CA A:HIS240 4.6 11.8 1.0 CG A:HIS240 4.7 10.8 1.0 O A:HOH435 4.7 23.8 1.0 CD A:GLU202 4.7 16.8 1.0 CB A:TYR67 4.7 10.3 1.0 O A:HOH457 4.8 16.2 1.0 C11 A:HML303 4.8 18.3 1.0 CA A:GLY241 4.8 13.0 1.0 CB A:PRO68 4.9 9.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Vim-2 Mbl in Complex with 1-(4-(Trifluoromethyl) Benzyl)-1H-Imidazole-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:28.9 occ:1.00 F19 A:HML303 0.0 28.9 1.0 C16 A:HML303 1.4 22.1 1.0 F18 A:HML303 2.2 23.9 1.0 F17 A:HML303 2.2 25.3 1.0 C13 A:HML303 2.4 18.0 1.0 C12 A:HML303 2.9 15.5 1.0 O A:HOH435 3.3 23.8 1.0 C14 A:HML303 3.6 16.0 1.0 OE2 A:GLU202 3.8 21.0 1.0 O A:HOH484 4.0 17.2 1.0 CD1 A:TYR67 4.1 14.3 1.0 C11 A:HML303 4.2 18.3 1.0 CE1 A:TYR67 4.4 14.3 1.0 C15 A:HML303 4.7 15.0 1.0 CD A:PRO68 4.8 9.1 1.0 CD A:ARG205 4.8 18.6 1.0 CD A:GLU202 5.0 16.8 1.0 C10 A:HML303 5.0 16.3 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