Fluorine in PDB 5y6d: Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11), PDB code: 5y6d was solved by G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.74 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	189.030, 39.832, 133.841, 90.00, 124.56, 90.00
R / Rfree (%)	16.2 / 21.9

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) also contains other interesting chemical elements:

Zinc

(Zn)

9 atoms

The binding sites of Fluorine atom in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) (pdb code 5y6d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11), PDB code: 5y6d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:24.3 occ:1.00 F08 A:8PL304 0.0 24.3 1.0 C05 A:8PL304 1.4 24.5 1.0 C04 A:8PL304 2.4 21.4 1.0 C06 A:8PL304 2.4 21.3 1.0 O B:ASP63 3.2 24.9 1.0 NE A:ARG205 3.4 29.4 1.0 CD2 A:TYR67 3.5 26.3 1.0 CE2 A:TYR67 3.6 29.7 1.0 CD A:ARG205 3.6 22.8 1.0 C B:GLY64 3.6 18.9 1.0 C03 A:8PL304 3.6 23.6 1.0 C07 A:8PL304 3.7 21.9 1.0 O B:HOH451 3.7 12.8 1.0 O B:GLY64 3.7 16.1 1.0 CG A:ARG205 3.9 25.1 1.0 CA B:GLY64 3.9 20.4 1.0 N B:ALA65 4.0 17.7 1.0 CZ A:ARG205 4.0 22.1 1.0 O A:HOH468 4.1 20.7 1.0 CB B:ALA65 4.1 19.3 1.0 C02 A:8PL304 4.1 22.1 1.0 C B:ASP63 4.2 21.5 1.0 CA B:ALA65 4.5 18.5 1.0 NH2 A:ARG205 4.5 21.3 1.0 N B:GLY64 4.5 18.8 1.0 NH1 A:ARG205 4.8 23.1 1.0 CG A:TYR67 4.8 18.0 1.0 CZ A:TYR67 4.9 29.0 1.0

Fluorine binding site 2 out of 4 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ B:F303 b:26.2 occ:1.00 F08 B:8PL303 0.0 26.2 1.0 C05 B:8PL303 1.4 22.4 1.0 C04 B:8PL303 2.4 22.5 1.0 C06 B:8PL303 2.4 21.1 1.0 O A:ASP63 3.0 22.1 1.0 C A:GLY64 3.2 21.3 1.0 CA A:GLY64 3.4 17.7 1.0 O A:GLY64 3.4 17.7 1.0 NE B:ARG205 3.6 15.6 1.0 N A:ALA65 3.6 14.3 1.0 C03 B:8PL303 3.7 19.8 1.0 C07 B:8PL303 3.7 20.9 1.0 O A:HOH422 3.7 11.8 1.0 CD2 B:TYR67 3.8 27.6 1.0 CB A:ALA65 3.9 16.9 1.0 CE2 B:TYR67 3.9 32.7 1.0 C A:ASP63 3.9 18.2 1.0 CD B:ARG205 3.9 18.1 1.0 N A:GLY64 4.1 15.7 1.0 CZ B:ARG205 4.1 16.2 1.0 C02 B:8PL303 4.2 20.6 1.0 CA A:ALA65 4.2 13.3 1.0 O B:HOH456 4.2 19.5 1.0 CG B:ARG205 4.3 16.6 1.0 NH2 B:ARG205 4.4 17.9 1.0 NH1 B:ARG205 4.9 14.8 1.0 OH A:TYR67 5.0 42.2 1.0

Fluorine binding site 3 out of 4 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ C:F303 b:32.3 occ:1.00 F08 C:8PL303 0.0 32.3 1.0 C05 C:8PL303 1.4 34.0 1.0 C04 C:8PL303 2.4 29.1 1.0 C06 C:8PL303 2.4 31.4 1.0 O D:ASP63 2.7 43.6 1.0 O D:HOH435 3.6 23.7 1.0 C D:GLY64 3.6 32.8 1.0 O D:GLY64 3.6 33.3 1.0 C03 C:8PL303 3.6 24.8 1.0 NE C:ARG205 3.7 30.4 1.0 C07 C:8PL303 3.7 28.9 1.0 CA D:GLY64 3.8 37.5 1.0 C D:ASP63 3.8 44.4 1.0 CD C:ARG205 3.9 35.3 1.0 CD2 C:TYR67 3.9 31.5 1.0 CE2 C:TYR67 4.0 32.7 1.0 N D:ALA65 4.0 24.4 1.0 CB D:ALA65 4.1 30.0 1.0 C02 C:8PL303 4.1 26.1 1.0 CZ C:ARG205 4.2 36.0 1.0 N D:GLY64 4.3 48.4 1.0 CG C:ARG205 4.3 26.2 1.0 O C:HOH449 4.4 31.9 1.0 CA D:ALA65 4.5 25.7 1.0 NH2 C:ARG205 4.6 30.6 1.0 NH1 C:ARG205 4.9 25.1 1.0

Fluorine binding site 4 out of 4 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range: probe atom residue distance (Å) B Occ D:F303 b:44.6 occ:1.00 F08 D:8PL303 0.0 44.6 1.0 C05 D:8PL303 1.4 47.3 1.0 C06 D:8PL303 2.4 38.2 1.0 C04 D:8PL303 2.4 40.6 1.0 O C:ASP63 2.9 36.3 1.0 CE2 D:TYR67 3.4 46.8 1.0 CD2 D:TYR67 3.4 42.3 1.0 NE D:ARG205 3.5 28.4 1.0 C C:GLY64 3.5 36.7 1.0 O C:GLY64 3.6 38.0 1.0 CA C:GLY64 3.7 36.6 1.0 C07 D:8PL303 3.7 41.1 1.0 C03 D:8PL303 3.7 35.6 1.0 CD D:ARG205 3.7 30.4 1.0 CB C:ALA65 3.9 32.6 1.0 CG D:ARG205 3.9 36.8 1.0 C C:ASP63 3.9 35.2 1.0 N C:ALA65 4.0 36.6 1.0 O D:HOH426 4.2 29.3 1.0 CZ D:ARG205 4.2 33.8 1.0 C02 D:8PL303 4.2 38.4 1.0 N C:GLY64 4.3 35.6 1.0 CA C:ALA65 4.5 33.2 1.0 NH2 D:ARG205 4.6 35.7 1.0 CZ D:TYR67 4.6 45.5 1.0 CG D:TYR67 4.7 41.5 1.0 NH1 D:ARG205 5.0 35.2 1.0

S.Liu, L.Jing, Z.-J.Yu, C.Wu, Y.Zheng, E.Zhang, Q.Chen, Y.Yu, L.Guo, Y.Wu, G.-B.Li. ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid Derivatives As Metallo-Beta-Lactamase Inhibitors: Synthesis, Kinetic and Crystallographic Studies. Eur J Med Chem V. 145 649 2018.
ISSN: ISSN 1768-3254
PubMed: 29353720
DOI: 10.1016/J.EJMECH.2018.01.032