Fluorine in PDB 6waa: K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
All present enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One):
5.6.2.2;
Protein crystallography data
The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa
was solved by
J.Noeske,
W.Shu,
C.Bellamacina,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
82.08 /
3.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.590,
157.481,
144.060,
90.00,
94.93,
90.00
|
R / Rfree (%)
|
27.4 /
30.1
|
Other elements in 6waa:
The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
(pdb code 6waa). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 1 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F101
b:78.7
occ:1.00
|
F
|
J:TNJ101
|
0.0
|
78.7
|
1.0
|
C3
|
J:TNJ101
|
1.3
|
77.9
|
1.0
|
C4
|
J:TNJ101
|
2.3
|
79.3
|
1.0
|
C2
|
J:TNJ101
|
2.4
|
76.0
|
1.0
|
C14
|
J:TNJ101
|
2.8
|
76.0
|
1.0
|
N2
|
J:TNJ101
|
2.9
|
74.8
|
1.0
|
N3
|
J:DC15
|
3.0
|
90.0
|
1.0
|
C5
|
J:DA16
|
3.1
|
82.5
|
1.0
|
C2
|
J:DC15
|
3.1
|
89.6
|
1.0
|
N7
|
J:DA16
|
3.1
|
87.0
|
1.0
|
C4
|
J:DC15
|
3.2
|
92.5
|
1.0
|
H2'
|
J:DC15
|
3.4
|
99.2
|
1.0
|
N1
|
J:DC15
|
3.4
|
91.1
|
1.0
|
C6
|
J:DA16
|
3.5
|
81.2
|
1.0
|
C8
|
J:DA16
|
3.5
|
85.4
|
1.0
|
C4
|
J:DA16
|
3.6
|
79.3
|
1.0
|
C5
|
J:DC15
|
3.6
|
95.0
|
1.0
|
C5
|
J:TNJ101
|
3.6
|
79.1
|
1.0
|
C6
|
J:DC15
|
3.6
|
93.8
|
1.0
|
O2
|
J:DC15
|
3.6
|
88.3
|
1.0
|
C1
|
J:TNJ101
|
3.6
|
75.8
|
1.0
|
C18
|
J:TNJ101
|
3.8
|
73.4
|
1.0
|
N9
|
J:DA16
|
3.8
|
80.9
|
1.0
|
H62
|
J:DA16
|
3.8
|
90.3
|
1.0
|
N6
|
J:DA16
|
3.9
|
84.2
|
1.0
|
N4
|
J:DC15
|
3.9
|
93.0
|
1.0
|
H8
|
J:DA16
|
4.0
|
94.3
|
1.0
|
C15
|
J:TNJ101
|
4.0
|
74.6
|
1.0
|
H42
|
J:DC15
|
4.1
|
96.7
|
1.0
|
C13
|
J:TNJ101
|
4.1
|
77.4
|
1.0
|
H5
|
J:DC15
|
4.1
|
95.0
|
1.0
|
N1
|
J:DA16
|
4.2
|
77.0
|
1.0
|
C2'
|
J:DC15
|
4.2
|
85.8
|
1.0
|
H1
|
K:DG12
|
4.2
|
97.0
|
1.0
|
H6
|
J:DC15
|
4.2
|
96.4
|
1.0
|
N3
|
J:DA16
|
4.3
|
76.2
|
1.0
|
C1'
|
J:DC15
|
4.3
|
90.3
|
1.0
|
H41
|
J:DC15
|
4.4
|
96.7
|
1.0
|
H22
|
K:DG12
|
4.5
|
0.3
|
1.0
|
H61
|
J:DA16
|
4.5
|
90.3
|
1.0
|
C2
|
J:DA16
|
4.5
|
75.3
|
1.0
|
C17
|
J:TNJ101
|
4.5
|
72.9
|
1.0
|
N1
|
K:DG12
|
4.7
|
0.6
|
1.0
|
H1'
|
J:DC15
|
4.7
|
0.2
|
1.0
|
O4'
|
J:DA16
|
4.7
|
81.2
|
1.0
|
H3'
|
J:DC15
|
4.7
|
99.5
|
1.0
|
C
|
J:TNJ101
|
4.8
|
75.5
|
1.0
|
H2''
|
J:DC15
|
4.8
|
99.2
|
1.0
|
C6
|
J:TNJ101
|
4.8
|
81.0
|
1.0
|
C1'
|
J:DA16
|
4.9
|
78.9
|
1.0
|
N2
|
K:DG12
|
4.9
|
0.8
|
1.0
|
C7
|
J:TNJ101
|
5.0
|
83.1
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6waa
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Fluorine Binding Sites List in 6waa
Fluorine binding site 2 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F101
b:83.4
occ:1.00
|
F1
|
J:TNJ101
|
0.0
|
83.4
|
1.0
|
C8
|
J:TNJ101
|
1.3
|
81.2
|
1.0
|
C9
|
J:TNJ101
|
2.3
|
80.5
|
1.0
|
C6
|
J:TNJ101
|
2.4
|
81.0
|
1.0
|
HB2
|
B:SER1080
|
2.5
|
71.5
|
1.0
|
HG
|
B:SER1080
|
2.5
|
75.3
|
1.0
|
O
|
J:TNJ101
|
2.7
|
81.8
|
1.0
|
C7
|
J:TNJ101
|
3.0
|
83.1
|
1.0
|
OG
|
B:SER1080
|
3.0
|
65.7
|
1.0
|
CB
|
B:SER1080
|
3.1
|
64.1
|
1.0
|
HB3
|
B:SER1080
|
3.4
|
71.5
|
1.0
|
N
|
J:TNJ101
|
3.4
|
83.7
|
1.0
|
H72
|
I:DT11
|
3.4
|
53.0
|
1.0
|
N7
|
K:DG12
|
3.4
|
96.7
|
1.0
|
N1
|
J:TNJ101
|
3.6
|
78.4
|
1.0
|
C5
|
J:TNJ101
|
3.7
|
79.1
|
1.0
|
H73
|
I:DT11
|
3.8
|
53.0
|
1.0
|
O6
|
K:DG12
|
4.0
|
1.0
|
1.0
|
O4
|
I:DT11
|
4.0
|
73.9
|
1.0
|
C7
|
I:DT11
|
4.0
|
64.5
|
1.0
|
C5
|
K:DG12
|
4.1
|
98.9
|
1.0
|
C13
|
J:TNJ101
|
4.1
|
77.4
|
1.0
|
H
|
B:SER1080
|
4.2
|
67.0
|
1.0
|
C8
|
K:DG12
|
4.3
|
95.5
|
1.0
|
C6
|
K:DG12
|
4.3
|
0.3
|
1.0
|
H8
|
K:DG12
|
4.4
|
87.8
|
1.0
|
CA
|
B:SER1080
|
4.5
|
63.9
|
1.0
|
HH12
|
D:ARG1119
|
4.5
|
0.9
|
1.0
|
C4
|
I:DT11
|
4.6
|
73.3
|
1.0
|
C5
|
I:DT11
|
4.6
|
68.8
|
1.0
|
C10
|
J:TNJ101
|
4.7
|
77.6
|
1.0
|
H
|
B:ALA1081
|
4.7
|
59.3
|
1.0
|
N
|
B:SER1080
|
4.8
|
62.8
|
1.0
|
C11
|
J:TNJ101
|
4.8
|
78.3
|
1.0
|
C4
|
J:TNJ101
|
4.8
|
79.3
|
1.0
|
H71
|
I:DT11
|
4.9
|
53.0
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6waa
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Fluorine Binding Sites List in 6waa
Fluorine binding site 3 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F102
b:0.7
occ:1.00
|
F
|
J:TNJ102
|
0.0
|
0.7
|
1.0
|
C3
|
J:TNJ102
|
1.3
|
0.5
|
1.0
|
C4
|
J:TNJ102
|
2.3
|
0.4
|
1.0
|
C2
|
J:TNJ102
|
2.4
|
0.4
|
1.0
|
C14
|
J:TNJ102
|
2.8
|
0.8
|
1.0
|
N2
|
J:TNJ102
|
2.9
|
0.6
|
1.0
|
C5
|
K:DA16
|
3.1
|
0.2
|
1.0
|
H2'
|
K:DC15
|
3.3
|
0.8
|
1.0
|
N7
|
K:DA16
|
3.3
|
0.3
|
1.0
|
C4
|
K:DA16
|
3.3
|
0.4
|
1.0
|
C8
|
K:DA16
|
3.5
|
0.4
|
1.0
|
C6
|
K:DA16
|
3.5
|
0.5
|
1.0
|
N9
|
K:DA16
|
3.6
|
0.5
|
1.0
|
C5
|
J:TNJ102
|
3.6
|
0.2
|
1.0
|
C18
|
J:TNJ102
|
3.6
|
0.7
|
1.0
|
C1
|
J:TNJ102
|
3.6
|
0.2
|
1.0
|
C2
|
K:DC15
|
3.7
|
0.9
|
1.0
|
N3
|
K:DC15
|
3.7
|
0.5
|
1.0
|
C15
|
J:TNJ102
|
3.8
|
0.9
|
1.0
|
N1
|
K:DC15
|
3.9
|
0.7
|
1.0
|
N3
|
K:DA16
|
3.9
|
0.7
|
1.0
|
O2
|
K:DC15
|
4.0
|
0.2
|
1.0
|
C4
|
K:DC15
|
4.0
|
0.6
|
1.0
|
H8
|
K:DA16
|
4.0
|
0.6
|
1.0
|
N1
|
K:DA16
|
4.1
|
0.8
|
1.0
|
C13
|
J:TNJ102
|
4.1
|
0.1
|
1.0
|
N6
|
K:DA16
|
4.1
|
0.4
|
1.0
|
C17
|
J:TNJ102
|
4.2
|
0.9
|
1.0
|
C2
|
K:DA16
|
4.2
|
0.8
|
1.0
|
C2'
|
K:DC15
|
4.2
|
0.9
|
1.0
|
H62
|
K:DA16
|
4.2
|
0.1
|
1.0
|
C6
|
K:DC15
|
4.2
|
0.4
|
1.0
|
O4'
|
K:DA16
|
4.2
|
0.9
|
1.0
|
C5
|
K:DC15
|
4.3
|
0.1
|
1.0
|
C1'
|
K:DA16
|
4.5
|
0.2
|
1.0
|
C1'
|
K:DC15
|
4.6
|
0.8
|
1.0
|
H2''
|
K:DC15
|
4.7
|
0.8
|
1.0
|
H61
|
K:DA16
|
4.7
|
0.1
|
1.0
|
N4
|
K:DC15
|
4.7
|
0.5
|
1.0
|
H6
|
K:DC15
|
4.7
|
0.8
|
1.0
|
H1
|
J:DG12
|
4.7
|
0.2
|
1.0
|
C
|
J:TNJ102
|
4.8
|
0.1
|
1.0
|
H1'
|
K:DA16
|
4.8
|
0.1
|
1.0
|
C6
|
J:TNJ102
|
4.8
|
0.0
|
1.0
|
H22
|
J:DG12
|
4.8
|
0.2
|
1.0
|
H3'
|
K:DC15
|
4.8
|
0.0
|
1.0
|
H5
|
K:DC15
|
4.8
|
0.1
|
1.0
|
H2
|
K:DA16
|
4.9
|
0.2
|
1.0
|
H1'
|
K:DC15
|
4.9
|
0.4
|
1.0
|
H42
|
K:DC15
|
4.9
|
0.2
|
1.0
|
N3
|
J:TNJ102
|
4.9
|
0.1
|
1.0
|
C7
|
J:TNJ102
|
5.0
|
0.1
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 4 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F102
b:0.7
occ:1.00
|
F1
|
J:TNJ102
|
0.0
|
0.7
|
1.0
|
C8
|
J:TNJ102
|
1.3
|
0.8
|
1.0
|
HG
|
D:SER1080
|
2.2
|
0.9
|
1.0
|
C9
|
J:TNJ102
|
2.3
|
0.7
|
1.0
|
C6
|
J:TNJ102
|
2.4
|
0.0
|
1.0
|
O
|
J:TNJ102
|
2.7
|
0.6
|
1.0
|
HB2
|
D:SER1080
|
2.8
|
0.7
|
1.0
|
OG
|
D:SER1080
|
2.8
|
95.4
|
1.0
|
C7
|
J:TNJ102
|
3.0
|
0.1
|
1.0
|
CB
|
D:SER1080
|
3.2
|
94.9
|
1.0
|
N7
|
J:DG12
|
3.2
|
1.0
|
1.0
|
N
|
J:TNJ102
|
3.3
|
0.1
|
1.0
|
HB3
|
D:SER1080
|
3.5
|
0.7
|
1.0
|
N1
|
J:TNJ102
|
3.6
|
0.9
|
1.0
|
C5
|
J:TNJ102
|
3.7
|
0.2
|
1.0
|
O6
|
J:DG12
|
3.7
|
99.9
|
1.0
|
C5
|
J:DG12
|
3.8
|
0.5
|
1.0
|
C6
|
J:DG12
|
4.0
|
0.9
|
1.0
|
C8
|
J:DG12
|
4.1
|
0.8
|
1.0
|
C13
|
J:TNJ102
|
4.1
|
0.1
|
1.0
|
H
|
D:SER1080
|
4.3
|
93.4
|
1.0
|
H8
|
J:DG12
|
4.4
|
1.0
|
1.0
|
O4
|
L:DT11
|
4.5
|
0.8
|
1.0
|
H72
|
L:DT11
|
4.6
|
99.7
|
1.0
|
CA
|
D:SER1080
|
4.6
|
93.5
|
1.0
|
C10
|
J:TNJ102
|
4.7
|
0.8
|
1.0
|
H42
|
K:DC15
|
4.8
|
0.2
|
1.0
|
C4
|
J:TNJ102
|
4.8
|
0.4
|
1.0
|
N
|
D:SER1080
|
4.9
|
93.0
|
1.0
|
C4
|
J:DG12
|
4.9
|
0.4
|
1.0
|
C11
|
J:TNJ102
|
4.9
|
0.7
|
1.0
|
H73
|
L:DT11
|
5.0
|
99.7
|
1.0
|
OD1
|
D:ASP1079
|
5.0
|
93.4
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 5 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:F101
b:0.8
occ:1.00
|
F
|
N:TNJ101
|
0.0
|
0.8
|
1.0
|
C3
|
N:TNJ101
|
1.3
|
1.0
|
1.0
|
C4
|
N:TNJ101
|
2.3
|
99.2
|
1.0
|
C2
|
N:TNJ101
|
2.4
|
0.1
|
1.0
|
C14
|
N:TNJ101
|
2.8
|
0.5
|
1.0
|
N2
|
N:TNJ101
|
2.9
|
0.6
|
1.0
|
C5
|
O:DA16
|
3.0
|
0.2
|
1.0
|
N7
|
O:DA16
|
3.2
|
0.4
|
1.0
|
C6
|
O:DA16
|
3.4
|
0.7
|
1.0
|
N3
|
O:DC15
|
3.4
|
0.2
|
1.0
|
C4
|
O:DA16
|
3.5
|
0.8
|
1.0
|
C4
|
O:DC15
|
3.5
|
0.2
|
1.0
|
C5
|
N:TNJ101
|
3.6
|
96.4
|
1.0
|
C2
|
O:DC15
|
3.6
|
0.1
|
1.0
|
C8
|
O:DA16
|
3.6
|
0.6
|
1.0
|
C1
|
N:TNJ101
|
3.6
|
98.6
|
1.0
|
H2'
|
O:DC15
|
3.7
|
0.9
|
1.0
|
N9
|
O:DA16
|
3.8
|
0.4
|
1.0
|
N6
|
O:DA16
|
3.8
|
0.9
|
1.0
|
C18
|
N:TNJ101
|
3.8
|
0.0
|
1.0
|
H62
|
O:DA16
|
3.8
|
92.7
|
1.0
|
C5
|
O:DC15
|
3.9
|
0.6
|
1.0
|
N1
|
O:DC15
|
3.9
|
0.1
|
1.0
|
N1
|
O:DA16
|
4.0
|
0.0
|
1.0
|
N4
|
O:DC15
|
4.0
|
0.3
|
1.0
|
C6
|
O:DC15
|
4.0
|
0.6
|
1.0
|
C13
|
N:TNJ101
|
4.1
|
95.7
|
1.0
|
N3
|
O:DA16
|
4.1
|
0.5
|
1.0
|
C15
|
N:TNJ101
|
4.1
|
0.2
|
1.0
|
O2
|
O:DC15
|
4.2
|
0.5
|
1.0
|
H8
|
O:DA16
|
4.2
|
0.7
|
1.0
|
H1
|
N:DG12
|
4.2
|
0.8
|
1.0
|
H42
|
O:DC15
|
4.2
|
0.2
|
1.0
|
C2
|
O:DA16
|
4.3
|
99.1
|
1.0
|
H61
|
O:DA16
|
4.4
|
92.7
|
1.0
|
H5
|
O:DC15
|
4.4
|
0.0
|
1.0
|
H22
|
N:DG12
|
4.4
|
0.2
|
1.0
|
H41
|
O:DC15
|
4.5
|
0.2
|
1.0
|
C17
|
N:TNJ101
|
4.6
|
0.5
|
1.0
|
H6
|
O:DC15
|
4.6
|
0.4
|
1.0
|
C2'
|
O:DC15
|
4.6
|
0.0
|
1.0
|
N1
|
N:DG12
|
4.6
|
0.1
|
1.0
|
O4'
|
O:DA16
|
4.7
|
0.8
|
1.0
|
C6
|
N:TNJ101
|
4.8
|
95.8
|
1.0
|
C
|
N:TNJ101
|
4.8
|
99.2
|
1.0
|
C1'
|
O:DA16
|
4.8
|
0.8
|
1.0
|
C1'
|
O:DC15
|
4.8
|
0.0
|
1.0
|
N2
|
N:DG12
|
4.9
|
98.9
|
1.0
|
H2
|
O:DA16
|
5.0
|
90.4
|
1.0
|
C7
|
N:TNJ101
|
5.0
|
98.0
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 6 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:F101
b:96.3
occ:1.00
|
F1
|
N:TNJ101
|
0.0
|
96.3
|
1.0
|
C8
|
N:TNJ101
|
1.3
|
94.7
|
1.0
|
HG
|
H:SER1080
|
2.3
|
0.5
|
1.0
|
C9
|
N:TNJ101
|
2.3
|
93.2
|
1.0
|
C6
|
N:TNJ101
|
2.4
|
95.8
|
1.0
|
HB2
|
H:SER1080
|
2.6
|
98.6
|
1.0
|
O
|
N:TNJ101
|
2.7
|
93.0
|
1.0
|
OG
|
H:SER1080
|
2.8
|
74.5
|
1.0
|
C7
|
N:TNJ101
|
3.0
|
98.0
|
1.0
|
CB
|
H:SER1080
|
3.2
|
72.8
|
1.0
|
N7
|
N:DG12
|
3.3
|
0.1
|
1.0
|
N1
|
N:TNJ101
|
3.6
|
93.5
|
1.0
|
HB3
|
H:SER1080
|
3.6
|
98.6
|
1.0
|
C5
|
N:TNJ101
|
3.7
|
96.4
|
1.0
|
N
|
N:TNJ101
|
3.8
|
98.5
|
1.0
|
H
|
H:SER1080
|
3.9
|
87.2
|
1.0
|
C5
|
N:DG12
|
3.9
|
0.4
|
1.0
|
C8
|
N:DG12
|
3.9
|
0.6
|
1.0
|
H72
|
P:DT11
|
4.0
|
0.1
|
1.0
|
HH12
|
F:ARG1119
|
4.1
|
0.5
|
1.0
|
H8
|
N:DG12
|
4.1
|
0.4
|
1.0
|
C13
|
N:TNJ101
|
4.1
|
95.7
|
1.0
|
O6
|
N:DG12
|
4.2
|
0.8
|
1.0
|
C6
|
N:DG12
|
4.3
|
0.4
|
1.0
|
CA
|
H:SER1080
|
4.5
|
72.2
|
1.0
|
OD1
|
H:ASP1079
|
4.5
|
73.2
|
1.0
|
N
|
H:SER1080
|
4.6
|
73.2
|
1.0
|
C10
|
N:TNJ101
|
4.6
|
93.0
|
1.0
|
C11
|
N:TNJ101
|
4.6
|
92.1
|
1.0
|
H73
|
P:DT11
|
4.6
|
0.1
|
1.0
|
C7
|
P:DT11
|
4.7
|
91.2
|
1.0
|
O4
|
P:DT11
|
4.8
|
97.3
|
1.0
|
H
|
H:ALA1081
|
4.8
|
84.7
|
1.0
|
C4
|
N:TNJ101
|
4.8
|
99.2
|
1.0
|
C4
|
N:DG12
|
4.9
|
0.9
|
1.0
|
N9
|
N:DG12
|
4.9
|
0.3
|
1.0
|
NH1
|
F:ARG1119
|
4.9
|
78.1
|
1.0
|
HH22
|
F:ARG1119
|
5.0
|
0.1
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 7 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:F102
b:81.5
occ:1.00
|
F
|
N:TNJ102
|
0.0
|
81.5
|
1.0
|
C3
|
N:TNJ102
|
1.3
|
80.2
|
1.0
|
C4
|
N:TNJ102
|
2.3
|
78.8
|
1.0
|
C2
|
N:TNJ102
|
2.4
|
80.4
|
1.0
|
C14
|
N:TNJ102
|
2.8
|
83.1
|
1.0
|
N2
|
N:TNJ102
|
2.9
|
81.8
|
1.0
|
H2'
|
N:DC15
|
3.0
|
96.3
|
1.0
|
C5
|
N:DA16
|
3.0
|
76.7
|
1.0
|
N7
|
N:DA16
|
3.1
|
80.6
|
1.0
|
C8
|
N:DA16
|
3.3
|
79.2
|
1.0
|
C4
|
N:DA16
|
3.3
|
73.9
|
1.0
|
C2
|
N:DC15
|
3.4
|
88.3
|
1.0
|
N9
|
N:DA16
|
3.5
|
75.2
|
1.0
|
N3
|
N:DC15
|
3.5
|
88.7
|
1.0
|
N1
|
N:DC15
|
3.6
|
89.1
|
1.0
|
C6
|
N:DA16
|
3.6
|
75.7
|
1.0
|
C5
|
N:TNJ102
|
3.6
|
77.6
|
1.0
|
C1
|
N:TNJ102
|
3.6
|
79.2
|
1.0
|
C18
|
N:TNJ102
|
3.7
|
82.8
|
1.0
|
C4
|
N:DC15
|
3.8
|
90.3
|
1.0
|
H8
|
N:DA16
|
3.8
|
77.0
|
1.0
|
O2
|
N:DC15
|
3.8
|
87.6
|
1.0
|
C6
|
N:DC15
|
3.8
|
91.1
|
1.0
|
C15
|
N:TNJ102
|
3.9
|
84.9
|
1.0
|
C2'
|
N:DC15
|
3.9
|
82.5
|
1.0
|
C5
|
N:DC15
|
4.0
|
92.2
|
1.0
|
N3
|
N:DA16
|
4.1
|
71.8
|
1.0
|
H62
|
N:DA16
|
4.1
|
77.3
|
1.0
|
C13
|
N:TNJ102
|
4.1
|
77.9
|
1.0
|
N6
|
N:DA16
|
4.1
|
78.2
|
1.0
|
O4'
|
N:DA16
|
4.2
|
75.8
|
1.0
|
N1
|
N:DA16
|
4.2
|
72.8
|
1.0
|
C1'
|
N:DC15
|
4.3
|
88.0
|
1.0
|
C17
|
N:TNJ102
|
4.3
|
84.7
|
1.0
|
H6
|
N:DC15
|
4.4
|
0.3
|
1.0
|
C2
|
N:DA16
|
4.4
|
71.6
|
1.0
|
H2''
|
N:DC15
|
4.4
|
96.3
|
1.0
|
C1'
|
N:DA16
|
4.5
|
73.5
|
1.0
|
H1
|
O:DG12
|
4.5
|
0.4
|
1.0
|
N4
|
N:DC15
|
4.5
|
90.4
|
1.0
|
H5
|
N:DC15
|
4.5
|
0.3
|
1.0
|
H3'
|
N:DC15
|
4.6
|
0.8
|
1.0
|
H1'
|
N:DC15
|
4.6
|
0.5
|
1.0
|
H22
|
O:DG12
|
4.7
|
0.2
|
1.0
|
H61
|
N:DA16
|
4.7
|
77.3
|
1.0
|
H42
|
N:DC15
|
4.8
|
0.2
|
1.0
|
C
|
N:TNJ102
|
4.8
|
79.5
|
1.0
|
C6
|
N:TNJ102
|
4.8
|
76.3
|
1.0
|
H1'
|
N:DA16
|
4.8
|
82.1
|
1.0
|
C3'
|
N:DC15
|
4.9
|
84.0
|
1.0
|
C7
|
N:TNJ102
|
5.0
|
76.1
|
1.0
|
H41
|
N:DC15
|
5.0
|
0.2
|
1.0
|
N1
|
O:DG12
|
5.0
|
93.1
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6waa
Go back to
Fluorine Binding Sites List in 6waa
Fluorine binding site 8 out
of 8 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:F102
b:74.5
occ:1.00
|
F1
|
N:TNJ102
|
0.0
|
74.5
|
1.0
|
C8
|
N:TNJ102
|
1.3
|
75.5
|
1.0
|
C9
|
N:TNJ102
|
2.3
|
75.9
|
1.0
|
C6
|
N:TNJ102
|
2.3
|
76.3
|
1.0
|
HB2
|
F:SER1080
|
2.5
|
76.3
|
1.0
|
O
|
N:TNJ102
|
2.7
|
75.5
|
1.0
|
HG
|
F:SER1080
|
2.9
|
76.7
|
1.0
|
C7
|
N:TNJ102
|
2.9
|
76.1
|
1.0
|
N
|
N:TNJ102
|
3.0
|
75.6
|
1.0
|
CB
|
F:SER1080
|
3.1
|
59.2
|
1.0
|
HB3
|
F:SER1080
|
3.1
|
76.3
|
1.0
|
OG
|
F:SER1080
|
3.3
|
61.9
|
1.0
|
N1
|
N:TNJ102
|
3.6
|
77.1
|
1.0
|
C5
|
N:TNJ102
|
3.6
|
77.6
|
1.0
|
O4
|
M:DT11
|
3.6
|
84.8
|
1.0
|
O6
|
O:DG12
|
3.7
|
87.6
|
1.0
|
N7
|
O:DG12
|
3.9
|
85.0
|
1.0
|
H73
|
M:DT11
|
3.9
|
60.9
|
1.0
|
H72
|
M:DT11
|
3.9
|
60.9
|
1.0
|
C13
|
N:TNJ102
|
4.1
|
77.9
|
1.0
|
C6
|
O:DG12
|
4.3
|
89.2
|
1.0
|
C7
|
M:DT11
|
4.3
|
73.8
|
1.0
|
C5
|
O:DG12
|
4.4
|
88.1
|
1.0
|
C4
|
M:DT11
|
4.4
|
79.4
|
1.0
|
CA
|
F:SER1080
|
4.5
|
58.7
|
1.0
|
H
|
F:ALA1081
|
4.6
|
65.6
|
1.0
|
H
|
F:SER1080
|
4.6
|
74.7
|
1.0
|
HH12
|
H:ARG1119
|
4.7
|
0.9
|
1.0
|
C10
|
N:TNJ102
|
4.7
|
77.6
|
1.0
|
H61
|
N:DA16
|
4.7
|
77.3
|
1.0
|
C5
|
M:DT11
|
4.8
|
74.0
|
1.0
|
H42
|
N:DC15
|
4.8
|
0.2
|
1.0
|
C4
|
N:TNJ102
|
4.8
|
78.8
|
1.0
|
N
|
F:ALA1081
|
4.9
|
55.3
|
1.0
|
C8
|
O:DG12
|
4.9
|
86.0
|
1.0
|
C11
|
N:TNJ102
|
4.9
|
77.4
|
1.0
|
C
|
F:SER1080
|
5.0
|
56.1
|
1.0
|
|
Reference:
C.K.Skepper,
D.Armstrong,
C.J.Balibar,
D.Bauer,
C.Bellamacina,
B.M.Benton,
D.Bussiere,
G.De Pascale,
J.De Vicente,
C.R.Dean,
B.Dhumale,
L.M.Fisher,
J.Fuller,
M.Fulsunder,
L.M.Holder,
C.Hu,
B.Kantariya,
G.Lapointe,
J.A.Leeds,
X.Li,
P.Lu,
A.Lvov,
S.Ma,
S.Madhavan,
S.Malekar,
D.Mckenney,
W.Mergo,
L.Metzger,
H.E.Moser,
D.Mutnick,
J.Noeske,
C.Osborne,
A.Patel,
D.Patel,
T.Patel,
K.Prajapati,
K.R.Prosen,
F.Reck,
D.L.Richie,
A.Rico,
M.R.Sanderson,
S.Satasia,
W.S.Sawyer,
J.Selvarajah,
N.Shah,
K.Shanghavi,
W.Shu,
K.V.Thompson,
M.Traebert,
A.Vala,
L.Vala,
D.A.Veselkov,
J.Vo,
M.Wang,
M.Widya,
S.L.Williams,
Y.Xu,
Q.Yue,
R.Zang,
B.Zhou,
A.Rivkin.
Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J.Med.Chem. V. 63 7773 2020.
ISSN: ISSN 0022-2623
PubMed: 32634310
DOI: 10.1021/ACS.JMEDCHEM.0C00347
Page generated: Fri Aug 2 03:40:00 2024
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