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)

Protein crystallography data

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

Other elements in 5y6d:

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

Fluorine Binding Sites:

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 5y6d

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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 5y6d

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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 5y6d

Go back to Fluorine Binding Sites List in 5y6d
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 5y6d

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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

Reference:

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
Page generated: Sun Dec 13 12:43:01 2020

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