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Fluorine in PDB 5acx: Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

Enzymatic activity of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

All present enzymatic activity of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening:
3.5.2.6;

Protein crystallography data

The structure of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acx was solved by T.Christopeit, T.J.O.Carlsen, R.Helland, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.61 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.230, 79.220, 67.640, 90.00, 130.18, 90.00
R / Rfree (%) 14.5 / 19.3

Other elements in 5acx:

The structure of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acx:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5acx

Go back to Fluorine Binding Sites List in 5acx
Fluorine binding site 1 out of 2 in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1298

b:48.2
occ:1.00
F13 A:WL31298 0.0 48.2 1.0
C06 A:WL31298 1.3 47.6 1.0
HB2 A:ASP119 2.3 28.1 0.4
C02 A:WL31298 2.3 46.9 1.0
C05 A:WL31298 2.4 47.9 1.0
H A:ASP119 2.5 21.2 1.0
H02 A:WL31298 2.5 56.2 1.0
H05 A:WL31298 2.6 57.4 1.0
HB2 A:ASP119 2.7 28.3 0.6
HB3 A:ASP119 2.7 28.3 0.6
CB A:ASP119 3.1 23.6 0.6
O A:HOH2135 3.1 21.7 1.0
CB A:ASP119 3.2 23.4 0.4
N A:ASP119 3.2 17.7 1.0
HB3 A:HIS118 3.4 17.2 1.0
OD2 A:ASP119 3.4 27.6 0.4
O A:HOH2083 3.5 32.1 1.0
C03 A:WL31298 3.6 46.4 1.0
C04 A:WL31298 3.6 47.3 1.0
CG A:ASP119 3.7 24.7 0.4
H A:ASP120 3.7 25.1 1.0
CA A:ASP119 3.7 20.8 0.6
CA A:ASP119 3.7 20.7 0.4
O A:HOH2078 3.7 37.7 1.0
HZ A:PHE61 3.8 73.4 0.8
HB3 A:ASP119 3.9 28.1 0.4
O A:HOH2188 4.0 41.0 1.0
C17 A:WL31298 4.1 46.5 1.0
CB A:HIS118 4.2 14.3 1.0
N A:ASP120 4.2 21.0 1.0
HA A:HIS118 4.3 18.2 1.0
C A:HIS118 4.3 15.8 1.0
HE1 A:TRP87 4.3 29.5 1.0
H03 A:WL31298 4.4 55.6 1.0
H04 A:WL31298 4.4 56.8 1.0
O A:HOH2139 4.4 26.0 1.0
C A:ASP119 4.4 20.9 1.0
CG A:ASP119 4.5 26.9 0.6
CZ A:PHE61 4.5 61.2 0.9
CA A:HIS118 4.5 15.2 1.0
HA A:ASP119 4.5 24.8 1.0
HE1 A:PHE61 4.6 73.2 0.7
OD1 A:ASP120 4.7 23.0 1.0
CG A:HIS118 4.8 16.3 1.0
OD1 A:ASP119 4.8 23.5 0.4
NE1 A:TRP87 4.8 24.6 1.0
OD2 A:ASP119 4.8 33.2 0.6
HZ2 A:TRP87 4.9 38.0 1.0
CE1 A:PHE61 4.9 61.0 0.8
HB2 A:HIS118 5.0 17.2 1.0
HB3 A:ASP120 5.0 35.8 1.0
HD22 A:ASN165 5.0 18.7 1.0

Fluorine binding site 2 out of 2 in 5acx

Go back to Fluorine Binding Sites List in 5acx
Fluorine binding site 2 out of 2 in the Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Vim-2-2, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1298

b:43.0
occ:1.00
F13 B:WL31298 0.0 43.0 1.0
C06 B:WL31298 1.3 41.1 1.0
HB2 B:ASP119 2.3 26.3 0.3
C02 B:WL31298 2.4 39.5 1.0
C05 B:WL31298 2.4 40.9 1.0
H02 B:WL31298 2.6 47.4 1.0
H05 B:WL31298 2.6 49.1 1.0
H B:ASP119 2.7 21.2 0.7
H B:ASP119 2.7 21.3 0.3
HB2 B:ASP119 2.8 27.0 0.7
HB3 B:ASP119 2.8 27.0 0.7
OD1 B:ASP119 3.2 34.1 0.3
CB B:ASP119 3.2 21.9 0.3
CB B:ASP119 3.2 22.5 0.7
O B:HOH2081 3.3 34.4 1.0
N B:ASP119 3.4 17.7 0.7
N B:ASP119 3.5 17.7 0.3
O B:HOH2128 3.5 24.0 1.0
CG B:ASP119 3.6 28.8 0.3
C03 B:WL31298 3.6 37.9 1.0
C04 B:WL31298 3.6 39.2 1.0
HB3 B:HIS118 3.7 22.1 1.0
HE1 B:TRP87 3.7 29.1 1.0
H B:ASP120 3.7 29.5 1.0
CA B:ASP119 3.8 22.1 0.7
CA B:ASP119 3.8 22.2 0.3
HB3 B:ASP119 3.9 26.3 0.3
HE1 B:PHE61 4.0 55.6 1.0
C17 B:WL31298 4.1 37.8 1.0
N B:ASP120 4.2 24.6 1.0
NE1 B:TRP87 4.3 24.3 1.0
C B:ASP119 4.4 21.5 0.7
HZ2 B:TRP87 4.4 36.2 1.0
H03 B:WL31298 4.4 45.5 1.0
H04 B:WL31298 4.4 47.1 1.0
C B:ASP119 4.4 21.6 0.3
O B:HOH2053 4.5 28.3 1.0
C B:HIS118 4.6 17.4 1.0
CG B:ASP119 4.6 31.9 0.7
CB B:HIS118 4.6 18.4 1.0
HA B:HIS118 4.7 23.5 1.0
HA B:ASP119 4.7 26.6 0.3
HA B:ASP119 4.7 26.5 0.7
CE1 B:PHE61 4.7 46.3 1.0
HD1 B:PHE61 4.7 55.4 1.0
OD1 B:ASP120 4.7 24.3 1.0
OD2 B:ASP119 4.8 31.4 0.3
CE2 B:TRP87 4.9 26.2 1.0
CZ2 B:TRP87 4.9 30.2 1.0
CA B:HIS118 4.9 19.6 1.0
HB3 B:ASP120 4.9 33.1 1.0
OD2 B:ASP119 4.9 43.4 0.7
O B:HOH2130 5.0 53.1 1.0

Reference:

T.Christopeit, T.J.O.Carlsen, R.Helland, H.K.S.Leiros. Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 By Spr Based Fragment Screening J.Med.Chem. V. 58 8671 2015.
ISSN: ISSN 0022-2623
PubMed: 26477515
DOI: 10.1021/ACS.JMEDCHEM.5B01289
Page generated: Sun Dec 13 12:18:03 2020

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