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Chlorine 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:

Fluorine (F) 2 atoms
Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5acx

Go back to Chlorine Binding Sites List in 5acx
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1300

b:30.0
occ:1.00
 ZN A:ZN1003 2.1 15.1 0.9
O A:HOH2163 2.9 31.0 1.0
HB3 A:ALA135 3.4 14.1 1.0
NE2 A:HIS170 3.5 13.6 1.0
CL A:CL1301 3.5 20.7 1.0
HB2 A:ALA135 3.6 14.1 1.0
CB A:ALA135 3.9 11.7 1.0
HH A:TYR137 4.0 21.5 1.0
CE1 A:HIS170 4.2 15.5 1.0
HE1 A:HIS170 4.2 18.6 1.0
CD2 A:HIS170 4.3 12.4 1.0
HB1 A:ALA135 4.4 14.1 1.0
OH A:TYR137 4.4 17.9 1.0
HD2 A:HIS170 4.5 14.9 1.0

Chlorine binding site 2 out of 4 in 5acx

Go back to Chlorine Binding Sites List in 5acx
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl1301

b:20.7
occ:1.00
 ZN A:ZN1003 2.2 15.1 0.9
HA A:ALA135 3.0 14.9 1.0
HB3 A:ALA135 3.2 14.1 1.0
HB2 A:ALA135 3.3 14.1 1.0
NE2 A:HIS170 3.3 13.6 1.0
CL A:CL1300 3.5 30.0 1.0
CB A:ALA135 3.6 11.7 1.0
HD2 A:HIS170 3.6 14.9 1.0
HG22 A:THR169 3.7 18.4 1.0
CA A:ALA135 3.7 12.4 1.0
CD2 A:HIS170 3.8 12.4 1.0
O A:HOH2161 4.1 14.3 1.0
HB A:THR169 4.3 19.3 1.0
H A:THR136 4.3 15.3 1.0
HG1 A:THR169 4.3 24.1 1.0
HB1 A:ALA135 4.5 14.1 1.0
CE1 A:HIS170 4.5 15.5 1.0
CG2 A:THR169 4.5 15.3 1.0
O A:HOH2155 4.6 20.6 1.0
N A:ALA135 4.6 13.7 1.0
O A:HOH2154 4.7 23.6 1.0
HG23 A:THR169 4.7 18.4 1.0
C A:ALA135 4.8 12.8 1.0
CB A:THR169 4.8 16.1 1.0
N A:THR136 4.8 12.8 1.0
HE1 A:HIS170 4.8 18.6 1.0
O A:VAL134 4.9 14.4 1.0
OG1 A:THR169 5.0 20.1 1.0

Chlorine binding site 3 out of 4 in 5acx

Go back to Chlorine Binding Sites List in 5acx
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl1300

b:30.8
occ:1.00
 ZN B:ZN1003 2.3 20.1 1.0
HE2 B:HIS170 2.4 29.8 1.0
O B:HOH2066 3.1 20.5 1.0
NE2 B:HIS170 3.3 24.8 1.0
HB3 B:ALA135 3.3 19.5 1.0
HA B:ALA135 3.4 19.7 1.0
CL B:CL1301 3.6 25.8 1.0
HB2 B:ALA135 3.7 19.5 1.0
CB B:ALA135 3.8 16.3 1.0
CA B:ALA135 4.0 16.4 1.0
HE1 B:HIS170 4.1 37.8 1.0
CE1 B:HIS170 4.1 31.5 1.0
CD2 B:HIS170 4.3 20.3 1.0
HD2 B:HIS170 4.4 24.4 1.0
HG22 B:THR169 4.5 33.0 1.0
O B:HOH2150 4.6 13.8 1.0
HB1 B:ALA135 4.7 19.5 1.0
N B:ALA135 4.8 17.7 1.0
H B:THR136 5.0 15.4 1.0

Chlorine binding site 4 out of 4 in 5acx

Go back to Chlorine Binding Sites List in 5acx
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1301

b:25.8
occ:1.00
 ZN B:ZN1003 2.2 20.1 1.0
O B:HOH2152 3.0 22.2 1.0
HE1 B:HIS170 3.1 37.8 1.0
HB3 B:ALA135 3.4 19.5 1.0
CE1 B:HIS170 3.5 31.5 1.0
HE2 B:HIS170 3.6 29.8 1.0
CL B:CL1300 3.6 30.8 1.0
HB2 B:ALA135 3.6 19.5 1.0
NE2 B:HIS170 3.8 24.8 1.0
CB B:ALA135 3.9 16.3 1.0
HH B:TYR137 4.0 31.0 1.0
HB1 B:ALA135 4.3 19.5 1.0
O B:HOH2068 4.4 37.6 1.0
OH B:TYR137 4.5 25.9 1.0
ND1 B:HIS170 4.5 32.4 1.0
CD2 B:HIS170 4.9 20.3 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 05:08:13 2024

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