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Chlorine in PDB 5acw: Vim-2-1, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

Enzymatic activity of Vim-2-1, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening

All present enzymatic activity of Vim-2-1, 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-2-1, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acw 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) 38.71 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.540, 79.290, 67.920, 90.00, 130.32, 90.00
R / Rfree (%) 14.2 / 19

Other elements in 5acw:

The structure of Vim-2-1, 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) 12 atoms
Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Vim-2-1, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening (pdb code 5acw). 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-2-1, Discovery of Novel Inhibitor Scaffolds Against the Metallo- Beta-Lactamase Vim-2 By Spr Based Fragment Screening, PDB code: 5acw:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5acw

Go back to Chlorine Binding Sites List in 5acw
Chlorine binding site 1 out of 4 in the Vim-2-1, 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-2-1, 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:17.2
occ:1.00
 ZN A:ZN1003 2.3 15.4 1.0
HA A:ALA135 3.0 15.3 1.0
NE2 A:HIS170 3.3 14.1 1.0
HB3 A:ALA135 3.4 17.4 1.0
HB2 A:ALA135 3.4 17.4 1.0
N02 A:RHU1299 3.4 40.6 0.7
HD2 A:HIS170 3.4 14.0 1.0
HG22 A:THR169 3.6 17.5 1.0
N03 A:RHU1299 3.6 37.0 0.7
CB A:ALA135 3.7 14.5 1.0
CD2 A:HIS170 3.7 11.7 1.0
CL A:CL1301 3.7 11.9 0.3
CA A:ALA135 3.8 12.8 1.0
O A:HOH2179 4.0 10.4 1.0
HB A:THR169 4.0 17.6 1.0
H A:THR136 4.1 13.7 1.0
CG2 A:THR169 4.3 14.6 1.0
HG23 A:THR169 4.3 17.5 1.0
CE1 A:HIS170 4.5 17.3 1.0
CB A:THR169 4.5 14.7 1.0
HB1 A:ALA135 4.6 17.4 1.0
C01 A:RHU1299 4.7 33.0 0.7
O A:HOH2172 4.7 22.4 1.0
OG1 A:THR169 4.7 16.5 1.0
N A:ALA135 4.7 11.5 1.0
N A:THR136 4.7 11.4 1.0
C A:ALA135 4.8 13.2 1.0
HG1 A:THR169 4.8 19.8 1.0
HE1 A:HIS170 4.8 20.8 1.0
C04 A:RHU1299 4.9 36.6 0.7
O A:VAL134 5.0 13.6 1.0

Chlorine binding site 2 out of 4 in 5acw

Go back to Chlorine Binding Sites List in 5acw
Chlorine binding site 2 out of 4 in the Vim-2-1, 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-2-1, 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:11.9
occ:0.33
 N02 A:RHU1299 0.3 40.6 0.7
N03 A:RHU1299 1.1 37.0 0.7
C01 A:RHU1299 1.2 33.0 0.7
C04 A:RHU1299 1.8 36.6 0.7
N05 A:RHU1299 1.9 33.8 0.7
ZN A:ZN1003 2.3 15.4 1.0
S06 A:RHU1299 2.8 27.8 0.7
HB3 A:ALA135 3.2 17.4 1.0
H061 A:RHU1299 3.2 33.4 0.7
C07 A:RHU1299 3.3 32.8 0.7
C08 A:RHU1299 3.3 32.7 0.7
HB2 A:ALA135 3.5 17.4 1.0
NE2 A:HIS170 3.6 14.1 1.0
CL A:CL1300 3.7 17.2 1.0
H07B A:RHU1299 3.8 39.3 0.7
CB A:ALA135 3.8 14.5 1.0
F10 A:RHU1299 3.9 35.1 0.7
H07A A:RHU1299 3.9 39.3 0.7
H07 A:RHU1299 4.0 39.3 0.7
F09 A:RHU1299 4.1 32.2 0.7
F11 A:RHU1299 4.1 24.1 0.7
HB1 A:ALA135 4.2 17.4 1.0
OH A:TYR137 4.3 17.0 1.0
CE1 A:HIS170 4.3 17.3 1.0
HE1 A:HIS170 4.3 20.8 1.0
HH A:TYR137 4.4 20.4 1.0
CD2 A:HIS170 4.5 11.7 1.0
HD2 A:HIS170 4.7 14.0 1.0

Chlorine binding site 3 out of 4 in 5acw

Go back to Chlorine Binding Sites List in 5acw
Chlorine binding site 3 out of 4 in the Vim-2-1, 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-2-1, 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:27.2
occ:1.00
 ZN B:ZN1003 2.2 18.4 1.0
HE2 B:HIS170 2.2 28.0 1.0
NE2 B:HIS170 3.1 23.4 1.0
O B:HOH2190 3.2 20.3 1.0
N02 B:RHU1299 3.2 43.6 0.7
N03 B:RHU1299 3.2 44.5 0.7
HA B:ALA135 3.4 19.8 1.0
HB3 B:ALA135 3.4 20.3 1.0
CL B:CL1301 3.4 11.3 0.3
HB2 B:ALA135 3.7 20.3 1.0
CB B:ALA135 3.9 16.9 1.0
CE1 B:HIS170 3.9 19.7 1.0
HE1 B:HIS170 3.9 23.6 1.0
CD2 B:HIS170 4.1 22.5 1.0
CA B:ALA135 4.1 16.5 1.0
HD2 B:HIS170 4.2 27.0 1.0
HG22 B:THR169 4.3 25.9 1.0
O B:HOH2158 4.4 22.0 1.0
C01 B:RHU1299 4.5 40.5 0.7
O B:HOH2167 4.5 12.2 1.0
C04 B:RHU1299 4.6 41.7 0.7
HG23 B:THR169 4.7 25.9 1.0
HB1 B:ALA135 4.8 20.3 1.0
H B:THR136 4.8 18.0 1.0
N B:ALA135 4.9 16.9 1.0
HB B:THR169 4.9 23.6 1.0
CG2 B:THR169 4.9 21.6 1.0

Chlorine binding site 4 out of 4 in 5acw

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Chlorine binding site 4 out of 4 in the Vim-2-1, 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-2-1, 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:11.3
occ:0.31
 N02 B:RHU1299 0.2 43.6 0.7
C01 B:RHU1299 1.1 40.5 0.7
N03 B:RHU1299 1.4 44.5 0.7
N05 B:RHU1299 2.1 41.4 0.7
ZN B:ZN1003 2.1 18.4 1.0
C04 B:RHU1299 2.1 41.7 0.7
S06 B:RHU1299 2.6 30.3 0.7
H061 B:RHU1299 2.8 36.4 0.7
HE1 B:HIS170 3.1 23.6 1.0
O B:HOH2168 3.2 33.7 1.0
HE2 B:HIS170 3.3 28.0 1.0
HB3 B:ALA135 3.3 20.3 1.0
CL B:CL1300 3.4 27.2 1.0
C07 B:RHU1299 3.5 40.3 0.7
CE1 B:HIS170 3.5 19.7 1.0
HB2 B:ALA135 3.5 20.3 1.0
HH B:TYR137 3.5 31.9 1.0
NE2 B:HIS170 3.5 23.4 1.0
C08 B:RHU1299 3.6 44.0 0.7
H07B B:RHU1299 3.8 48.4 0.7
CB B:ALA135 3.8 16.9 1.0
H07A B:RHU1299 4.1 48.4 0.7
H07 B:RHU1299 4.1 48.4 0.7
OH B:TYR137 4.2 26.6 1.0
F10 B:RHU1299 4.2 50.1 0.7
HB1 B:ALA135 4.3 20.3 1.0
F09 B:RHU1299 4.3 43.0 0.7
F11 B:RHU1299 4.4 45.5 0.7
ND1 B:HIS170 4.5 23.4 1.0
CD2 B:HIS170 4.6 22.5 1.0
HA B:ALA135 5.0 19.8 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 05:07:28 2024

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