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

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

All present enzymatic activity of Vim-2-Ox, 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-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acv 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) 25.63 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.709, 79.484, 66.845, 90.00, 129.92, 90.00
R / Rfree (%) 16.2 / 20.9

Other elements in 5acv:

The structure of Vim-2-Ox, 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) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Vim-2-Ox, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5acv

Go back to Chlorine Binding Sites List in 5acv
Chlorine binding site 1 out of 4 in the Vim-2-Ox, 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 Chlorine with other atoms in the Cl binding site number 1 of Vim-2-Ox, 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:Cl1300

b:17.5
occ:1.00
 ZN A:ZN1299 2.3 15.2 1.0
HA A:ALA135 2.9 16.1 1.0
HB3 A:ALA135 3.2 17.4 1.0
HB2 A:ALA135 3.3 17.4 1.0
NE2 A:HIS170 3.5 13.9 1.0
CB A:ALA135 3.6 14.5 1.0
CL A:CL1301 3.6 40.4 1.0
HD2 A:HIS170 3.6 15.2 1.0
CA A:ALA135 3.7 13.4 1.0
HG22 A:THR169 3.8 20.2 1.0
CD2 A:HIS170 3.9 12.7 1.0
O A:HOH2157 4.0 14.6 1.0
H A:THR136 4.2 15.2 1.0
HB A:THR169 4.3 18.9 1.0
O A:HOH2154 4.3 12.9 1.0
HG1 A:THR169 4.4 19.3 1.0
HB1 A:ALA135 4.5 17.4 1.0
N A:ALA135 4.6 12.9 1.0
O A:HOH2048 4.6 29.7 1.0
CG2 A:THR169 4.6 16.8 1.0
CE1 A:HIS170 4.7 14.4 1.0
C A:ALA135 4.7 12.6 1.0
N A:THR136 4.8 12.6 1.0
HG23 A:THR169 4.8 20.2 1.0
O A:VAL134 4.8 12.7 1.0
CB A:THR169 4.9 15.7 1.0
H A:ALA135 5.0 15.5 1.0

Chlorine binding site 2 out of 4 in 5acv

Go back to Chlorine Binding Sites List in 5acv
Chlorine binding site 2 out of 4 in the Vim-2-Ox, 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 Chlorine with other atoms in the Cl binding site number 2 of Vim-2-Ox, 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:Cl1301

b:40.4
occ:1.00
 ZN A:ZN1299 2.1 15.2 1.0
O A:HOH2048 3.0 29.7 1.0
HB3 A:ALA135 3.2 17.4 1.0
HB2 A:ALA135 3.4 17.4 1.0
NE2 A:HIS170 3.4 13.9 1.0
CL A:CL1300 3.6 17.5 1.0
CB A:ALA135 3.7 14.5 1.0
OH A:TYR137 4.0 16.7 1.0
CE1 A:HIS170 4.1 14.4 1.0
HB1 A:ALA135 4.2 17.4 1.0
HH A:TYR137 4.2 20.0 1.0
HE1 A:HIS170 4.2 17.3 1.0
CD2 A:HIS170 4.2 12.7 1.0
HD2 A:HIS170 4.4 15.2 1.0
HA A:ALA135 4.9 16.1 1.0

Chlorine binding site 3 out of 4 in 5acv

Go back to Chlorine Binding Sites List in 5acv
Chlorine binding site 3 out of 4 in the Vim-2-Ox, 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 Chlorine with other atoms in the Cl binding site number 3 of Vim-2-Ox, 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:Cl1300

b:18.7
occ:0.92
 ZN B:ZN1299 2.2 18.9 1.0
O B:HOH2173 3.0 26.9 1.0
HA B:ALA135 3.1 14.2 1.0
NE2 B:HIS170 3.4 17.1 1.0
CL B:CL1301 3.5 32.6 0.7
HB3 B:ALA135 3.5 15.6 1.0
HB2 B:ALA135 3.7 15.6 1.0
HD2 B:HIS170 3.8 18.7 1.0
HG22 B:THR169 3.8 22.2 1.0
CB B:ALA135 3.9 13.0 1.0
CA B:ALA135 3.9 11.8 1.0
CD2 B:HIS170 4.0 15.6 1.0
O B:HOH2149 4.2 14.2 1.0
O B:HOH2048 4.3 26.7 1.0
H B:THR136 4.5 14.0 1.0
HB B:THR169 4.5 20.7 1.0
CE1 B:HIS170 4.5 17.7 1.0
HG1 B:THR169 4.6 21.9 1.0
CG2 B:THR169 4.6 18.5 1.0
N B:ALA135 4.7 11.7 1.0
HE1 B:HIS170 4.8 21.3 1.0
HG23 B:THR169 4.8 22.2 1.0
HB1 B:ALA135 4.8 15.6 1.0
O B:VAL134 4.8 11.7 1.0
CB B:THR169 5.0 17.3 1.0

Chlorine binding site 4 out of 4 in 5acv

Go back to Chlorine Binding Sites List in 5acv
Chlorine binding site 4 out of 4 in the Vim-2-Ox, 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 Chlorine with other atoms in the Cl binding site number 4 of Vim-2-Ox, 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:Cl1301

b:32.6
occ:0.74
 ZN B:ZN1299 2.2 18.9 1.0
O B:HOH2292 2.4 22.4 1.0
O B:HOH2048 2.5 26.7 1.0
HB3 B:ALA135 2.9 15.6 1.0
HB2 B:ALA135 3.3 15.6 1.0
CL B:CL1300 3.5 18.7 0.9
NE2 B:HIS170 3.5 17.1 1.0
CB B:ALA135 3.5 13.0 1.0
HH B:TYR137 3.9 22.1 1.0
HB1 B:ALA135 4.0 15.6 1.0
HE1 B:HIS170 4.0 21.3 1.0
CE1 B:HIS170 4.1 17.7 1.0
O B:HOH2150 4.3 47.7 1.0
OH B:TYR137 4.3 18.4 1.0
CD2 B:HIS170 4.4 15.6 1.0
HA B:ALA135 4.6 14.2 1.0
HD2 B:HIS170 4.6 18.7 1.0
CA B:ALA135 4.7 11.8 1.0
O B:HOH2113 5.0 24.4 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: Fri Jul 26 05:06:45 2024

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