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Fluorine in PDB 5le1: Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16), PDB code: 5le1 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) 41.02 / 1.40
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 45.171, 60.720, 97.911, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 15.4

Other elements in 5le1:

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) (pdb code 5le1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16), PDB code: 5le1:

Fluorine binding site 1 out of 1 in 5le1

Go back to Fluorine Binding Sites List in 5le1
Fluorine binding site 1 out of 1 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16)


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 2-(2-Chloro-6- Fluorobenzyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:21.9
occ:1.00
F21 A:6UW503 0.0 21.9 1.0
C20 A:6UW503 1.3 25.4 1.0
C15 A:6UW503 2.3 19.0 1.0
C19 A:6UW503 2.4 29.8 1.0
C14 A:6UW503 2.8 18.4 1.0
ND2 A:ASN210 2.9 24.4 1.0
O A:HOH654 3.0 25.9 1.0
N12 A:6UW503 3.5 14.7 1.0
C16 A:6UW503 3.6 18.5 1.0
O11 A:6UW503 3.6 19.2 1.0
C18 A:6UW503 3.6 28.2 1.0
O A:HOH794 3.7 24.1 1.0
CG A:ASN210 3.8 22.9 1.0
C10 A:6UW503 3.9 16.6 1.0
CZ A:PHE62 3.9 29.9 1.0
CE1 A:PHE62 4.0 26.1 1.0
O A:HOH907 4.0 48.1 1.0
C17 A:6UW503 4.1 25.0 1.0
O A:HOH931 4.3 54.3 1.0
O A:HOH781 4.5 46.7 1.0
OD1 A:ASN210 4.5 24.7 1.0
CE1 A:HIS116 4.6 15.0 1.0
CB A:ASN210 4.6 19.8 1.0
C13 A:6UW503 4.6 16.3 1.0
ND1 A:HIS116 4.7 13.1 1.0
NE2 A:HIS116 4.8 15.7 1.0
CG A:HIS116 4.9 12.4 1.0
CD2 A:HIS116 5.0 13.7 1.0

Reference:

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
Page generated: Tue Jul 15 04:59:13 2025

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