Fluorine in PDB 8pie: Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
Enzymatic activity of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
All present enzymatic activity of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010:
2.7.13.3;
2.7.4.6;
Protein crystallography data
The structure of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010, PDB code: 8pie
was solved by
M.Feracci,
A.Chazot,
F.Ferron,
K.Alvarez,
B.Canard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.68 /
1.90
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.19,
120.313,
71.918,
90,
110.15,
90
|
|
R / Rfree (%)
|
17.2 /
21.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
(pdb code 8pie). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010, PDB code: 8pie:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:42.4
occ:1.00
|
F4
|
A:7QT201
|
0.0
|
42.4
|
1.0
|
|
C2'
|
A:7QT201
|
1.4
|
47.9
|
1.0
|
|
H1
|
A:7QT201
|
2.3
|
44.6
|
1.0
|
|
C1'
|
A:7QT201
|
2.4
|
47.5
|
1.0
|
|
C3'
|
A:7QT201
|
2.4
|
47.2
|
1.0
|
|
C3
|
A:7QT201
|
2.5
|
47.4
|
1.0
|
|
H3
|
A:7QT201
|
2.5
|
47.5
|
1.0
|
|
H6
|
A:7QT201
|
2.7
|
51.0
|
1.0
|
|
O3'
|
A:7QT201
|
2.7
|
43.8
|
1.0
|
|
H2
|
A:7QT201
|
2.9
|
47.4
|
1.0
|
|
C4'
|
A:7QT201
|
2.9
|
53.2
|
1.0
|
|
H16
|
A:7QT201
|
3.0
|
43.7
|
0.0
|
|
O4'
|
A:7QT201
|
3.0
|
42.8
|
1.0
|
|
HZ3
|
A:LYS16
|
3.0
|
22.3
|
1.0
|
|
HZ1
|
A:LYS16
|
3.1
|
22.3
|
1.0
|
|
H4
|
A:7QT201
|
3.2
|
47.5
|
1.0
|
|
H5
|
A:7QT201
|
3.3
|
47.6
|
1.0
|
|
O
|
A:HOH373
|
3.3
|
40.6
|
1.0
|
|
HD11
|
A:LEU68
|
3.5
|
33.6
|
1.0
|
|
NZ
|
A:LYS16
|
3.5
|
22.6
|
1.0
|
|
HD12
|
A:LEU68
|
3.5
|
33.6
|
1.0
|
|
HH
|
A:TYR56
|
3.6
|
26.9
|
0.0
|
|
HE1
|
A:TYR56
|
3.7
|
21.8
|
1.0
|
|
N9
|
A:7QT201
|
3.7
|
38.5
|
1.0
|
|
HZ2
|
A:LYS16
|
3.9
|
22.3
|
1.0
|
|
O
|
A:HOH301
|
3.9
|
35.7
|
1.0
|
|
CD1
|
A:LEU68
|
3.9
|
34.9
|
1.0
|
|
HD22
|
A:LEU68
|
4.0
|
31.2
|
1.0
|
|
HD23
|
A:LEU68
|
4.0
|
31.3
|
1.0
|
|
OH
|
A:TYR56
|
4.0
|
27.1
|
1.0
|
|
O1P
|
A:HIP122
|
4.0
|
73.4
|
1.0
|
|
CE1
|
A:TYR56
|
4.2
|
21.1
|
1.0
|
|
O3P
|
A:HIP122
|
4.3
|
70.5
|
1.0
|
|
O2P
|
A:HIP122
|
4.3
|
83.1
|
1.0
|
|
CZ
|
A:TYR56
|
4.3
|
23.2
|
1.0
|
|
C5'
|
A:7QT201
|
4.4
|
60.0
|
1.0
|
|
CD2
|
A:LEU68
|
4.4
|
31.3
|
1.0
|
|
N3
|
A:7QT201
|
4.4
|
26.4
|
1.0
|
|
P
|
A:HIP122
|
4.5
|
56.6
|
1.0
|
|
C4
|
A:7QT201
|
4.5
|
30.9
|
1.0
|
|
HD13
|
A:LEU68
|
4.6
|
33.5
|
1.0
|
|
HD22
|
A:ASN119
|
4.7
|
18.8
|
1.0
|
|
HE2
|
A:LYS16
|
4.7
|
21.5
|
1.0
|
|
H7
|
A:7QT201
|
4.7
|
59.1
|
1.0
|
|
CE
|
A:LYS16
|
4.7
|
21.6
|
1.0
|
|
C8
|
A:7QT201
|
4.8
|
38.2
|
1.0
|
|
CG
|
A:LEU68
|
4.8
|
31.1
|
1.0
|
|
H8
|
A:7QT201
|
4.9
|
59.1
|
1.0
|
|
HD11
|
A:LEU59
|
4.9
|
38.7
|
1.0
|
|
H9
|
A:7QT201
|
4.9
|
39.2
|
1.0
|
|
O5'
|
A:7QT201
|
5.0
|
62.8
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F201
b:43.7
occ:1.00
|
F4
|
B:7QT201
|
0.0
|
43.7
|
1.0
|
|
C2'
|
B:7QT201
|
1.4
|
53.1
|
1.0
|
|
C1'
|
B:7QT201
|
2.3
|
46.5
|
1.0
|
|
H1
|
B:7QT201
|
2.4
|
47.6
|
1.0
|
|
C3
|
B:7QT201
|
2.4
|
47.8
|
1.0
|
|
H3
|
B:7QT201
|
2.4
|
49.2
|
1.0
|
|
C3'
|
B:7QT201
|
2.5
|
57.9
|
1.0
|
|
H6
|
B:7QT201
|
2.8
|
61.4
|
1.0
|
|
O3'
|
B:7QT201
|
2.8
|
47.1
|
1.0
|
|
O4'
|
B:7QT201
|
2.8
|
54.1
|
1.0
|
|
H2
|
B:7QT201
|
2.9
|
49.0
|
1.0
|
|
C4'
|
B:7QT201
|
2.9
|
62.8
|
1.0
|
|
HZ3
|
B:LYS16
|
3.0
|
20.8
|
1.0
|
|
H16
|
B:7QT201
|
3.0
|
47.4
|
0.0
|
|
HZ1
|
B:LYS16
|
3.1
|
20.8
|
1.0
|
|
H4
|
B:7QT201
|
3.2
|
49.2
|
1.0
|
|
O
|
B:HOH350
|
3.3
|
44.7
|
1.0
|
|
H5
|
B:7QT201
|
3.3
|
55.4
|
1.0
|
|
O
|
B:HOH302
|
3.3
|
40.1
|
1.0
|
|
NZ
|
B:LYS16
|
3.5
|
20.6
|
1.0
|
|
HD12
|
B:LEU68
|
3.5
|
45.9
|
1.0
|
|
HD11
|
B:LEU68
|
3.5
|
45.9
|
1.0
|
|
N9
|
B:7QT201
|
3.6
|
40.9
|
1.0
|
|
HH
|
B:TYR56
|
3.7
|
40.1
|
0.0
|
|
HE1
|
B:TYR56
|
3.8
|
33.5
|
1.0
|
|
HZ2
|
B:LYS16
|
3.8
|
20.8
|
1.0
|
|
CD1
|
B:LEU68
|
4.0
|
49.7
|
1.0
|
|
O3P
|
B:HIP122
|
4.0
|
51.1
|
1.0
|
|
HD22
|
B:LEU68
|
4.0
|
38.5
|
1.0
|
|
HD23
|
B:LEU68
|
4.1
|
38.5
|
1.0
|
|
OH
|
B:TYR56
|
4.1
|
40.4
|
1.0
|
|
CE1
|
B:TYR56
|
4.2
|
32.5
|
1.0
|
|
O2P
|
B:HIP122
|
4.3
|
94.0
|
1.0
|
|
O1P
|
B:HIP122
|
4.4
|
57.9
|
1.0
|
|
C5'
|
B:7QT201
|
4.4
|
70.5
|
1.0
|
|
C4
|
B:7QT201
|
4.4
|
35.8
|
1.0
|
|
CZ
|
B:TYR56
|
4.5
|
38.2
|
1.0
|
|
CD2
|
B:LEU68
|
4.5
|
38.6
|
1.0
|
|
N3
|
B:7QT201
|
4.5
|
34.0
|
1.0
|
|
P
|
B:HIP122
|
4.5
|
60.7
|
1.0
|
|
HD22
|
B:ASN119
|
4.5
|
20.6
|
1.0
|
|
HD13
|
B:LEU68
|
4.6
|
45.7
|
1.0
|
|
HE2
|
B:LYS16
|
4.7
|
20.1
|
1.0
|
|
C8
|
B:7QT201
|
4.7
|
47.8
|
1.0
|
|
CE
|
B:LYS16
|
4.7
|
21.4
|
1.0
|
|
H9
|
B:7QT201
|
4.8
|
44.9
|
1.0
|
|
H7
|
B:7QT201
|
4.8
|
72.2
|
1.0
|
|
H8
|
B:7QT201
|
4.8
|
72.1
|
1.0
|
|
CG
|
B:LEU68
|
4.9
|
38.1
|
1.0
|
|
HG22
|
B:THR98
|
4.9
|
34.3
|
1.0
|
|
OD1
|
B:ASN119
|
4.9
|
19.7
|
1.0
|
|
HD12
|
B:LEU59
|
4.9
|
36.9
|
1.0
|
|
HD11
|
B:LEU59
|
4.9
|
36.8
|
1.0
|
|
O
|
B:HOH305
|
4.9
|
37.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:75.9
occ:1.00
|
F4
|
C:7QT201
|
0.0
|
75.9
|
1.0
|
|
C2'
|
C:7QT201
|
1.5
|
56.0
|
1.0
|
|
H3
|
C:7QT201
|
2.2
|
55.8
|
1.0
|
|
C3
|
C:7QT201
|
2.3
|
55.7
|
1.0
|
|
H1
|
C:7QT201
|
2.4
|
58.6
|
1.0
|
|
C1'
|
C:7QT201
|
2.4
|
62.7
|
1.0
|
|
C3'
|
C:7QT201
|
2.5
|
55.6
|
1.0
|
|
HZ1
|
C:LYS16
|
2.7
|
16.2
|
1.0
|
|
H4
|
C:7QT201
|
2.9
|
55.7
|
1.0
|
|
O3'
|
C:7QT201
|
2.9
|
61.0
|
1.0
|
|
HD12
|
C:LEU68
|
3.0
|
28.2
|
1.0
|
|
H6
|
C:7QT201
|
3.0
|
67.4
|
1.0
|
|
HZ3
|
C:LYS16
|
3.0
|
16.2
|
1.0
|
|
H2
|
C:7QT201
|
3.1
|
55.4
|
1.0
|
|
HD11
|
C:LEU68
|
3.1
|
28.2
|
1.0
|
|
C4'
|
C:7QT201
|
3.1
|
68.4
|
1.0
|
|
H16
|
C:7QT201
|
3.2
|
60.7
|
0.0
|
|
O4'
|
C:7QT201
|
3.2
|
63.5
|
1.0
|
|
NZ
|
C:LYS16
|
3.3
|
15.5
|
1.0
|
|
H5
|
C:7QT201
|
3.3
|
59.2
|
1.0
|
|
CD1
|
C:LEU68
|
3.5
|
29.8
|
1.0
|
|
N9
|
C:7QT201
|
3.6
|
48.4
|
1.0
|
|
HH
|
C:TYR56
|
3.6
|
28.2
|
0.0
|
|
HZ2
|
C:LYS16
|
3.7
|
16.2
|
1.0
|
|
OH
|
C:TYR56
|
4.0
|
28.0
|
1.0
|
|
N3
|
C:7QT201
|
4.0
|
43.1
|
1.0
|
|
HD13
|
C:LEU68
|
4.1
|
28.1
|
1.0
|
|
HD23
|
C:LEU68
|
4.1
|
29.2
|
1.0
|
|
HD22
|
C:LEU68
|
4.1
|
29.2
|
1.0
|
|
C4
|
C:7QT201
|
4.2
|
39.9
|
1.0
|
|
HE1
|
C:TYR56
|
4.2
|
30.0
|
1.0
|
|
O
|
C:HOH307
|
4.2
|
32.4
|
1.0
|
|
O3P
|
C:HIP122
|
4.4
|
55.6
|
1.0
|
|
HE2
|
C:LYS16
|
4.5
|
16.8
|
1.0
|
|
CD2
|
C:LEU68
|
4.5
|
31.2
|
1.0
|
|
CZ
|
C:TYR56
|
4.5
|
27.4
|
1.0
|
|
CE
|
C:LYS16
|
4.5
|
18.1
|
1.0
|
|
CE1
|
C:TYR56
|
4.5
|
31.4
|
1.0
|
|
O2P
|
C:HIP122
|
4.6
|
60.2
|
1.0
|
|
HE2
|
C:TYR71
|
4.6
|
24.0
|
1.0
|
|
C5'
|
C:7QT201
|
4.6
|
83.6
|
1.0
|
|
CG
|
C:LEU68
|
4.6
|
24.8
|
1.0
|
|
HD22
|
C:ASN119
|
4.6
|
19.7
|
1.0
|
|
OD1
|
C:ASN119
|
4.7
|
20.8
|
1.0
|
|
C8
|
C:7QT201
|
4.8
|
47.9
|
1.0
|
|
H7
|
C:7QT201
|
4.9
|
84.3
|
1.0
|
|
HD3
|
C:LYS16
|
4.9
|
16.2
|
1.0
|
|
P
|
C:HIP122
|
4.9
|
56.5
|
1.0
|
|
O1P
|
C:HIP122
|
5.0
|
87.4
|
1.0
|
|
O
|
C:VAL116
|
5.0
|
19.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F201
b:40.4
occ:1.00
|
F4
|
D:7QT201
|
0.0
|
40.4
|
1.0
|
|
C2'
|
D:7QT201
|
1.4
|
48.0
|
1.0
|
|
H1
|
D:7QT201
|
2.2
|
52.4
|
1.0
|
|
C1'
|
D:7QT201
|
2.2
|
51.0
|
1.0
|
|
H6
|
D:7QT201
|
2.3
|
66.4
|
1.0
|
|
C3'
|
D:7QT201
|
2.3
|
54.5
|
1.0
|
|
O
|
D:HOH308
|
2.5
|
31.1
|
1.0
|
|
C4'
|
D:7QT201
|
2.5
|
71.0
|
1.0
|
|
C3
|
D:7QT201
|
2.5
|
46.7
|
1.0
|
|
H3
|
D:7QT201
|
2.6
|
47.1
|
1.0
|
|
O3'
|
D:7QT201
|
2.6
|
50.1
|
1.0
|
|
H16
|
D:7QT201
|
2.7
|
51.2
|
0.0
|
|
O4'
|
D:7QT201
|
2.7
|
59.4
|
1.0
|
|
H2
|
D:7QT201
|
3.0
|
47.1
|
1.0
|
|
H5
|
D:7QT201
|
3.2
|
55.2
|
1.0
|
|
H4
|
D:7QT201
|
3.3
|
47.1
|
1.0
|
|
HZ3
|
D:LYS16
|
3.3
|
18.4
|
1.0
|
|
HZ1
|
D:LYS16
|
3.3
|
18.4
|
1.0
|
|
HD12
|
D:LEU68
|
3.5
|
27.2
|
1.0
|
|
N9
|
D:7QT201
|
3.6
|
53.9
|
1.0
|
|
HH
|
D:TYR56
|
3.6
|
27.6
|
0.0
|
|
HE1
|
D:TYR56
|
3.7
|
27.4
|
1.0
|
|
O
|
D:HOH371
|
3.7
|
32.4
|
1.0
|
|
HD11
|
D:LEU68
|
3.7
|
27.2
|
1.0
|
|
NZ
|
D:LYS16
|
3.8
|
18.5
|
1.0
|
|
O
|
D:HOH301
|
3.8
|
33.6
|
1.0
|
|
C5'
|
D:7QT201
|
4.0
|
79.1
|
1.0
|
|
CD1
|
D:LEU68
|
4.0
|
28.2
|
1.0
|
|
HD23
|
D:LEU68
|
4.1
|
28.2
|
1.0
|
|
OH
|
D:TYR56
|
4.1
|
27.4
|
1.0
|
|
HD22
|
D:LEU68
|
4.1
|
28.2
|
1.0
|
|
CE1
|
D:TYR56
|
4.1
|
30.2
|
1.0
|
|
HZ2
|
D:LYS16
|
4.2
|
18.4
|
1.0
|
|
O3P
|
D:HIP122
|
4.2
|
54.5
|
1.0
|
|
N3
|
D:7QT201
|
4.2
|
49.4
|
1.0
|
|
O1P
|
D:HIP122
|
4.3
|
78.6
|
1.0
|
|
C4
|
D:7QT201
|
4.3
|
46.0
|
1.0
|
|
H7
|
D:7QT201
|
4.3
|
79.3
|
1.0
|
|
CZ
|
D:TYR56
|
4.4
|
26.7
|
1.0
|
|
O2P
|
D:HIP122
|
4.5
|
43.5
|
1.0
|
|
H8
|
D:7QT201
|
4.5
|
79.7
|
1.0
|
|
CD2
|
D:LEU68
|
4.5
|
29.6
|
1.0
|
|
P
|
D:HIP122
|
4.5
|
46.6
|
1.0
|
|
C8
|
D:7QT201
|
4.7
|
54.9
|
1.0
|
|
O5'
|
D:7QT201
|
4.7
|
89.7
|
1.0
|
|
HD13
|
D:LEU68
|
4.7
|
27.2
|
1.0
|
|
H9
|
D:7QT201
|
4.9
|
55.8
|
1.0
|
|
HE2
|
D:LYS16
|
4.9
|
18.5
|
1.0
|
|
HD12
|
D:LEU59
|
4.9
|
33.2
|
1.0
|
|
CE
|
D:LYS16
|
4.9
|
18.3
|
1.0
|
|
CG
|
D:LEU68
|
5.0
|
25.2
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F201
b:51.2
occ:1.00
|
F4
|
E:7QT201
|
0.0
|
51.2
|
1.0
|
|
C2'
|
E:7QT201
|
1.4
|
67.0
|
1.0
|
|
H3
|
E:7QT201
|
2.3
|
65.1
|
1.0
|
|
H1
|
E:7QT201
|
2.3
|
62.7
|
1.0
|
|
C1'
|
E:7QT201
|
2.4
|
65.7
|
1.0
|
|
C3
|
E:7QT201
|
2.4
|
64.6
|
1.0
|
|
C3'
|
E:7QT201
|
2.5
|
62.2
|
1.0
|
|
H6
|
E:7QT201
|
2.6
|
67.0
|
1.0
|
|
C4'
|
E:7QT201
|
2.8
|
67.9
|
1.0
|
|
O3'
|
E:7QT201
|
2.9
|
65.1
|
1.0
|
|
O4'
|
E:7QT201
|
2.9
|
58.2
|
1.0
|
|
H4
|
E:7QT201
|
3.0
|
65.2
|
1.0
|
|
H2
|
E:7QT201
|
3.1
|
64.9
|
1.0
|
|
HZ1
|
E:LYS16
|
3.1
|
21.1
|
1.0
|
|
HD11
|
E:LEU68
|
3.1
|
29.6
|
1.0
|
|
H16
|
E:7QT201
|
3.1
|
65.3
|
0.0
|
|
HZ3
|
E:LYS16
|
3.2
|
21.2
|
1.0
|
|
HD12
|
E:LEU68
|
3.2
|
29.6
|
1.0
|
|
H5
|
E:7QT201
|
3.3
|
64.6
|
1.0
|
|
NZ
|
E:LYS16
|
3.6
|
22.5
|
1.0
|
|
HH
|
E:TYR56
|
3.6
|
22.9
|
0.0
|
|
CD1
|
E:LEU68
|
3.6
|
27.4
|
1.0
|
|
N9
|
E:7QT201
|
3.7
|
58.0
|
1.0
|
|
HD23
|
E:LEU68
|
3.8
|
33.5
|
1.0
|
|
HE1
|
E:TYR56
|
3.8
|
25.2
|
1.0
|
|
HD22
|
E:LEU68
|
3.9
|
33.5
|
1.0
|
|
OH
|
E:TYR56
|
4.0
|
22.8
|
1.0
|
|
HZ2
|
E:LYS16
|
4.0
|
21.1
|
1.0
|
|
CE1
|
E:TYR56
|
4.1
|
24.0
|
1.0
|
|
CD2
|
E:LEU68
|
4.2
|
32.7
|
1.0
|
|
N3
|
E:7QT201
|
4.2
|
43.0
|
1.0
|
|
CZ
|
E:TYR56
|
4.2
|
27.8
|
1.0
|
|
O3P
|
E:HIP122
|
4.3
|
56.2
|
1.0
|
|
C5'
|
E:7QT201
|
4.3
|
81.0
|
1.0
|
|
HD13
|
E:LEU68
|
4.4
|
29.5
|
1.0
|
|
C4
|
E:7QT201
|
4.4
|
45.9
|
1.0
|
|
O1P
|
E:HIP122
|
4.4
|
48.6
|
1.0
|
|
O2P
|
E:HIP122
|
4.5
|
72.8
|
1.0
|
|
CG
|
E:LEU68
|
4.6
|
35.5
|
1.0
|
|
P
|
E:HIP122
|
4.6
|
58.0
|
1.0
|
|
H7
|
E:7QT201
|
4.7
|
81.2
|
1.0
|
|
HE2
|
E:LYS16
|
4.7
|
19.4
|
1.0
|
|
CE
|
E:LYS16
|
4.8
|
18.5
|
1.0
|
|
H8
|
E:7QT201
|
4.8
|
81.3
|
1.0
|
|
C8
|
E:7QT201
|
4.8
|
51.5
|
1.0
|
|
HD12
|
E:LEU59
|
5.0
|
40.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8pie
Go back to
Fluorine Binding Sites List in 8pie
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Human Nucleoside Diphosphate Kinase B Domain in Complex with the Product at-8500 Formed By Catalysis of Compound at-9010 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F201
b:58.4
occ:1.00
|
F4
|
F:7QT201
|
0.0
|
58.4
|
1.0
|
|
C2'
|
F:7QT201
|
1.4
|
69.2
|
1.0
|
|
H1
|
F:7QT201
|
2.3
|
69.9
|
1.0
|
|
C1'
|
F:7QT201
|
2.3
|
71.4
|
1.0
|
|
C3'
|
F:7QT201
|
2.3
|
65.4
|
1.0
|
|
H6
|
F:7QT201
|
2.4
|
71.5
|
1.0
|
|
H3
|
F:7QT201
|
2.4
|
65.9
|
1.0
|
|
C3
|
F:7QT201
|
2.4
|
64.6
|
1.0
|
|
O
|
F:HOH302
|
2.5
|
31.4
|
1.0
|
|
O3'
|
F:7QT201
|
2.6
|
67.5
|
1.0
|
|
C4'
|
F:7QT201
|
2.7
|
72.4
|
1.0
|
|
H16
|
F:7QT201
|
2.8
|
67.6
|
0.0
|
|
O4'
|
F:7QT201
|
2.8
|
64.2
|
1.0
|
|
H2
|
F:7QT201
|
2.9
|
66.0
|
1.0
|
|
HZ3
|
F:LYS16
|
3.0
|
19.8
|
1.0
|
|
HZ1
|
F:LYS16
|
3.1
|
19.7
|
1.0
|
|
H4
|
F:7QT201
|
3.2
|
65.9
|
1.0
|
|
H5
|
F:7QT201
|
3.2
|
67.9
|
1.0
|
|
NZ
|
F:LYS16
|
3.4
|
19.9
|
1.0
|
|
N9
|
F:7QT201
|
3.6
|
73.5
|
1.0
|
|
HH
|
F:TYR56
|
3.6
|
34.3
|
0.0
|
|
HD11
|
F:LEU68
|
3.7
|
29.9
|
1.0
|
|
HD12
|
F:LEU68
|
3.7
|
29.9
|
1.0
|
|
HZ2
|
F:LYS16
|
3.8
|
19.7
|
1.0
|
|
HE1
|
F:TYR56
|
3.9
|
27.6
|
1.0
|
|
O1P
|
F:HIP122
|
4.0
|
48.4
|
1.0
|
|
OH
|
F:TYR56
|
4.1
|
34.1
|
1.0
|
|
C5'
|
F:7QT201
|
4.2
|
85.4
|
1.0
|
|
CD1
|
F:LEU68
|
4.2
|
29.4
|
1.0
|
|
O2P
|
F:HIP122
|
4.3
|
77.8
|
1.0
|
|
N3
|
F:7QT201
|
4.3
|
74.3
|
1.0
|
|
C4
|
F:7QT201
|
4.4
|
69.6
|
1.0
|
|
O3P
|
F:HIP122
|
4.4
|
75.3
|
1.0
|
|
CE1
|
F:TYR56
|
4.4
|
26.6
|
1.0
|
|
HD23
|
F:LEU68
|
4.5
|
30.9
|
1.0
|
|
H7
|
F:7QT201
|
4.5
|
86.8
|
1.0
|
|
P
|
F:HIP122
|
4.5
|
48.9
|
1.0
|
|
HD22
|
F:LEU68
|
4.5
|
30.9
|
1.0
|
|
H8
|
F:7QT201
|
4.6
|
87.0
|
1.0
|
|
CZ
|
F:TYR56
|
4.6
|
27.8
|
1.0
|
|
HD22
|
F:ASN119
|
4.6
|
20.4
|
1.0
|
|
HE2
|
F:LYS16
|
4.6
|
19.0
|
1.0
|
|
CE
|
F:LYS16
|
4.7
|
19.5
|
1.0
|
|
C8
|
F:7QT201
|
4.7
|
73.3
|
1.0
|
|
O
|
F:HOH312
|
4.8
|
36.1
|
1.0
|
|
HD13
|
F:LEU68
|
4.8
|
29.9
|
1.0
|
|
H9
|
F:7QT201
|
4.8
|
71.9
|
1.0
|
|
CD2
|
F:LEU68
|
4.9
|
30.9
|
1.0
|
|
OD1
|
F:ASN119
|
4.9
|
20.6
|
1.0
|
|
Reference:
A.Chazot,
C.Zimberger,
M.Feracci,
A.Moussa,
S.Good,
J.P.Sommadossi,
K.Alvarez,
F.Ferron,
B.Canard.
The Activation Chain of the Broad-Spectrum Antiviral Bemnifosbuvir at Atomic Resolution Plos Biol. 2024.
ISSN: ESSN 1545-7885
DOI: 10.1371/JOURNAL.PBIO.3002743
Page generated: Sun Aug 11 11:19:34 2024
|
