Fluorine in PDB 5lca: Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17)

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17), PDB code: 5lca was solved by G.-B.Li, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.99 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.487, 65.313, 70.716, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 17

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17) (pdb code 5lca). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17), PDB code: 5lca:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17)


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 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:42.3 occ:1.00 F21 A:B06503 0.0 42.3 1.0 C20 A:B06503 1.4 38.9 1.0 F22 A:B06503 2.2 41.4 1.0 F23 A:B06503 2.2 41.1 1.0 C18 A:B06503 2.4 28.7 1.0 C17 A:B06503 2.7 26.1 1.0 NE2 A:HIS116 2.9 12.7 1.0 O A:HOH709 3.0 28.6 1.0 O A:HOH629 3.0 25.7 1.0 CD2 A:HIS116 3.1 11.1 1.0 OD2 A:ASP213 3.3 18.0 1.0 CE1 A:HIS116 3.5 12.8 1.0 C19 A:B06503 3.6 23.9 1.0 CG A:HIS116 3.8 10.0 1.0 ND1 A:HIS116 4.0 12.2 1.0 C16 A:B06503 4.1 24.3 1.0 O A:HOH720 4.2 11.1 1.0 CG A:ASP213 4.5 18.3 1.0 C14 A:B06503 4.7 20.4 1.0 ND2 A:ASN210 4.7 42.8 1.0 CB A:HIS116 4.8 9.1 1.0 C15 A:B06503 5.0 22.7 1.0

Fluorine binding site 2 out of 3 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17)


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 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:41.4 occ:1.00 F22 A:B06503 0.0 41.4 1.0 C20 A:B06503 1.4 38.9 1.0 F23 A:B06503 2.2 41.1 1.0 F21 A:B06503 2.2 42.3 1.0 C18 A:B06503 2.4 28.7 1.0 ND2 A:ASN210 2.8 42.8 1.0 C19 A:B06503 3.1 23.9 1.0 C17 A:B06503 3.3 26.1 1.0 CG A:ASN210 3.7 37.2 1.0 OD1 A:ASN210 4.0 36.2 1.0 CZ A:PHE62 4.1 27.8 1.0 C14 A:B06503 4.4 20.4 1.0 CE1 A:PHE62 4.4 26.3 1.0 C16 A:B06503 4.5 24.3 1.0 O A:HOH604 4.5 44.3 1.0 O A:HOH629 4.6 25.7 1.0 NE2 A:HIS116 4.7 12.7 1.0 OD2 A:ASP213 4.7 18.0 1.0 O A:HOH709 4.8 28.6 1.0 CE1 A:HIS116 4.9 12.8 1.0 CB A:ASN210 4.9 29.3 1.0 C15 A:B06503 4.9 22.7 1.0

Fluorine binding site 3 out of 3 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17)


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 3-Oxo-2-(3- (Trifluoromethyl)Phenyl)Isoindoline-4-Carboxylic Acid (Compound 17) within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:41.1 occ:1.00 F23 A:B06503 0.0 41.1 1.0 C20 A:B06503 1.4 38.9 1.0 F22 A:B06503 2.2 41.4 1.0 F21 A:B06503 2.2 42.3 1.0 C18 A:B06503 2.4 28.7 1.0 C19 A:B06503 2.8 23.9 1.0 CE1 A:HIS116 2.9 12.8 1.0 NE2 A:HIS116 3.1 12.7 1.0 ND2 A:ASN210 3.3 42.8 1.0 CG A:ASN210 3.4 37.2 1.0 OD1 A:ASN210 3.5 36.2 1.0 OD2 A:ASP213 3.6 18.0 1.0 C17 A:B06503 3.6 26.1 1.0 ND1 A:HIS116 3.7 12.2 1.0 CD2 A:HIS116 3.9 11.1 1.0 O A:HOH673 4.0 22.4 1.0 C14 A:B06503 4.1 20.4 1.0 CG A:HIS116 4.2 10.0 1.0 O12 A:B06503 4.3 14.9 1.0 CB A:ASN210 4.3 29.3 1.0 CG A:ASP213 4.5 18.3 1.0 O A:HOH629 4.7 25.7 1.0 C16 A:B06503 4.7 24.3 1.0 CB A:ASP213 4.9 16.8 1.0 C15 A:B06503 4.9 22.7 1.0 ZN A:ZN501 5.0 11.8 1.0 C11 A:B06503 5.0 15.6 1.0

G.B.Li, M.I.Abboud, J.Brem, H.Someya, C.T.Lohans, S.Y.Yang, J.Spencer, D.W.Wareham, M.A.Mcdonough, C.J.Schofield. uc(Nmr)-Filtered Virtual Screening Leads to Non-Metal Chelating Metallo-Beta-Lactamase Inhibitors. Chem Sci V. 8 928 2017.
ISSN: ISSN 2041-6520
PubMed: 28451231
DOI: 10.1039/C6SC04524C