Fluorine in PDB 8pyw: Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
Enzymatic activity of Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
All present enzymatic activity of Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.:
2.7.13.3;
2.7.4.6;
Protein crystallography data
The structure of Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp., PDB code: 8pyw
was solved by
M.Feracci,
A.Chazot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.67 /
1.55
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.22,
121.06,
70.76,
90,
107.14,
90
|
|
R / Rfree (%)
|
17 /
20
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
(pdb code 8pyw). 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 Bound to Compound Diphosphate Form of at-9052-Sp., PDB code: 8pyw:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F202
b:37.9
occ:1.00
|
F1
|
A:IF9202
|
0.0
|
37.9
|
1.0
|
|
C2'
|
A:IF9202
|
1.4
|
35.4
|
1.0
|
|
H1'
|
A:IF9202
|
2.3
|
37.1
|
1.0
|
|
C1'
|
A:IF9202
|
2.3
|
35.5
|
1.0
|
|
C3'
|
A:IF9202
|
2.4
|
40.3
|
1.0
|
|
C1
|
A:IF9202
|
2.4
|
42.2
|
1.0
|
|
H4'
|
A:IF9202
|
2.5
|
49.0
|
1.0
|
|
H2
|
A:IF9202
|
2.5
|
39.1
|
1.0
|
|
C4'
|
A:IF9202
|
2.7
|
55.4
|
1.0
|
|
O3'
|
A:IF9202
|
2.8
|
38.6
|
1.0
|
|
H1
|
A:IF9202
|
2.8
|
39.9
|
1.0
|
|
HO3'
|
A:IF9202
|
2.9
|
30.0
|
0.0
|
|
O
|
A:HOH335
|
2.9
|
32.8
|
1.0
|
|
O4'
|
A:IF9202
|
2.9
|
50.3
|
1.0
|
|
H3
|
A:IF9202
|
3.2
|
40.1
|
1.0
|
|
HZ3
|
A:LYS16
|
3.3
|
19.5
|
1.0
|
|
H3'
|
A:IF9202
|
3.3
|
42.0
|
1.0
|
|
HZ1
|
A:LYS16
|
3.3
|
19.5
|
1.0
|
|
O
|
A:HOH310
|
3.5
|
30.8
|
1.0
|
|
O
|
A:HOH424
|
3.6
|
31.0
|
1.0
|
|
N9
|
A:IF9202
|
3.6
|
32.9
|
1.0
|
|
HD12
|
A:LEU68
|
3.7
|
27.4
|
1.0
|
|
NZ
|
A:LYS16
|
3.7
|
19.9
|
1.0
|
|
HE1
|
A:TYR56
|
3.9
|
21.9
|
1.0
|
|
HD23
|
A:LEU68
|
3.9
|
30.3
|
1.0
|
|
HH
|
A:TYR56
|
3.9
|
30.0
|
0.0
|
|
HZ2
|
A:LYS16
|
4.0
|
19.0
|
1.0
|
|
HD22
|
A:LEU68
|
4.1
|
31.1
|
1.0
|
|
HD11
|
A:LEU68
|
4.2
|
26.6
|
1.0
|
|
C5'
|
A:IF9202
|
4.2
|
47.0
|
1.0
|
|
CD1
|
A:LEU68
|
4.4
|
30.5
|
1.0
|
|
CE1
|
A:TYR56
|
4.4
|
22.9
|
1.0
|
|
CD2
|
A:LEU68
|
4.4
|
35.8
|
1.0
|
|
C4
|
A:IF9202
|
4.5
|
30.2
|
1.0
|
|
N3'
|
A:IF9202
|
4.5
|
28.3
|
1.0
|
|
OH
|
A:TYR56
|
4.5
|
26.7
|
1.0
|
|
H5'
|
A:IF9202
|
4.5
|
50.9
|
1.0
|
|
HD22
|
A:ASN119
|
4.6
|
16.0
|
1.0
|
|
HD11
|
A:LEU59
|
4.6
|
29.1
|
1.0
|
|
O
|
A:HOH302
|
4.6
|
32.4
|
1.0
|
|
C5
|
A:IF9202
|
4.7
|
38.2
|
1.0
|
|
H5''
|
A:IF9202
|
4.7
|
51.4
|
1.0
|
|
H8
|
A:IF9202
|
4.7
|
37.8
|
1.0
|
|
HD12
|
A:LEU59
|
4.8
|
30.0
|
1.0
|
|
CZ
|
A:TYR56
|
4.8
|
22.6
|
1.0
|
|
HG21
|
A:THR98
|
4.9
|
27.4
|
0.5
|
|
HG22
|
A:THR98
|
4.9
|
26.4
|
0.5
|
|
O
|
A:HOH351
|
5.0
|
29.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F202
b:39.6
occ:1.00
|
F1
|
B:IF9202
|
0.0
|
39.6
|
1.0
|
|
C2'
|
B:IF9202
|
1.4
|
36.8
|
1.0
|
|
C1'
|
B:IF9202
|
2.3
|
29.7
|
1.0
|
|
H1'
|
B:IF9202
|
2.3
|
31.6
|
1.0
|
|
C1
|
B:IF9202
|
2.4
|
35.5
|
1.0
|
|
C3'
|
B:IF9202
|
2.4
|
39.5
|
1.0
|
|
H2
|
B:IF9202
|
2.5
|
34.8
|
1.0
|
|
H4'
|
B:IF9202
|
2.6
|
38.0
|
1.0
|
|
H1
|
B:IF9202
|
2.8
|
35.9
|
1.0
|
|
C4'
|
B:IF9202
|
2.8
|
42.3
|
1.0
|
|
O3'
|
B:IF9202
|
2.9
|
38.7
|
1.0
|
|
O4'
|
B:IF9202
|
2.9
|
33.9
|
1.0
|
|
HZ3
|
B:LYS16
|
3.1
|
23.4
|
1.0
|
|
O
|
B:HOH308
|
3.1
|
39.3
|
1.0
|
|
HO3'
|
B:IF9202
|
3.2
|
30.0
|
0.0
|
|
H3
|
B:IF9202
|
3.2
|
36.0
|
1.0
|
|
HZ1
|
B:LYS16
|
3.3
|
23.5
|
1.0
|
|
H3'
|
B:IF9202
|
3.3
|
39.8
|
1.0
|
|
HD12
|
B:LEU68
|
3.4
|
32.9
|
1.0
|
|
O
|
B:HOH373
|
3.5
|
33.0
|
1.0
|
|
O
|
B:HOH424
|
3.6
|
42.2
|
1.0
|
|
NZ
|
B:LYS16
|
3.6
|
23.5
|
1.0
|
|
O
|
B:HOH312
|
3.6
|
40.6
|
1.0
|
|
N9
|
B:IF9202
|
3.6
|
30.6
|
1.0
|
|
HZ2
|
B:LYS16
|
3.8
|
23.0
|
1.0
|
|
O
|
B:HOH305
|
3.9
|
29.7
|
1.0
|
|
HE1
|
B:TYR56
|
4.0
|
22.2
|
1.0
|
|
HH
|
B:TYR56
|
4.1
|
30.0
|
0.0
|
|
HD23
|
B:LEU68
|
4.1
|
34.3
|
1.0
|
|
HD22
|
B:LEU68
|
4.2
|
35.2
|
1.0
|
|
C5'
|
B:IF9202
|
4.3
|
35.4
|
1.0
|
|
CD1
|
B:LEU68
|
4.3
|
36.8
|
1.0
|
|
HD22
|
B:ASN119
|
4.4
|
18.6
|
1.0
|
|
C4
|
B:IF9202
|
4.5
|
33.8
|
1.0
|
|
CE1
|
B:TYR56
|
4.5
|
20.9
|
1.0
|
|
HG22
|
B:THR98
|
4.5
|
24.9
|
0.5
|
|
N3'
|
B:IF9202
|
4.5
|
27.1
|
1.0
|
|
OH
|
B:TYR56
|
4.5
|
29.3
|
1.0
|
|
HD11
|
B:LEU68
|
4.6
|
32.2
|
1.0
|
|
H5'
|
B:IF9202
|
4.6
|
39.6
|
1.0
|
|
C5
|
B:IF9202
|
4.6
|
33.7
|
1.0
|
|
CD2
|
B:LEU68
|
4.6
|
39.4
|
1.0
|
|
H8
|
B:IF9202
|
4.7
|
33.9
|
1.0
|
|
HD11
|
B:LEU59
|
4.7
|
27.0
|
1.0
|
|
H5''
|
B:IF9202
|
4.8
|
40.5
|
1.0
|
|
HD13
|
B:LEU68
|
4.8
|
32.8
|
1.0
|
|
ND2
|
B:ASN119
|
4.8
|
18.0
|
1.0
|
|
HD12
|
B:LEU59
|
4.8
|
27.9
|
1.0
|
|
CZ
|
B:TYR56
|
4.8
|
27.0
|
1.0
|
|
HG21
|
B:THR98
|
4.9
|
26.4
|
0.5
|
|
CE
|
B:LYS16
|
4.9
|
21.4
|
1.0
|
|
OD1
|
B:ASN119
|
4.9
|
20.7
|
1.0
|
|
HE2
|
B:LYS16
|
4.9
|
21.2
|
1.0
|
|
HE1
|
B:PHE64
|
5.0
|
30.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:28.1
occ:1.00
|
F1
|
C:IF9201
|
0.0
|
28.1
|
1.0
|
|
C2'
|
C:IF9201
|
1.4
|
27.1
|
1.0
|
|
C1
|
C:IF9201
|
2.2
|
29.1
|
1.0
|
|
H2
|
C:IF9201
|
2.3
|
27.8
|
1.0
|
|
H1'
|
C:IF9201
|
2.4
|
24.2
|
1.0
|
|
C1'
|
C:IF9201
|
2.4
|
22.9
|
1.0
|
|
C3'
|
C:IF9201
|
2.4
|
30.0
|
1.0
|
|
H1
|
C:IF9201
|
2.6
|
28.4
|
1.0
|
|
O3'
|
C:IF9201
|
2.7
|
26.4
|
1.0
|
|
H4'
|
C:IF9201
|
2.7
|
27.8
|
1.0
|
|
C4'
|
C:IF9201
|
2.9
|
29.3
|
1.0
|
|
HO3'
|
C:IF9201
|
3.0
|
30.0
|
0.0
|
|
O4'
|
C:IF9201
|
3.1
|
26.7
|
1.0
|
|
H3
|
C:IF9201
|
3.1
|
28.8
|
1.0
|
|
HZ3
|
C:LYS16
|
3.1
|
17.1
|
1.0
|
|
O
|
C:HOH344
|
3.2
|
23.5
|
1.0
|
|
O
|
C:HOH313
|
3.3
|
27.1
|
1.0
|
|
H3'
|
C:IF9201
|
3.3
|
29.1
|
1.0
|
|
HZ1
|
C:LYS16
|
3.3
|
17.1
|
1.0
|
|
NZ
|
C:LYS16
|
3.6
|
17.6
|
1.0
|
|
N9
|
C:IF9201
|
3.6
|
24.7
|
1.0
|
|
O
|
C:HOH413
|
3.7
|
28.4
|
1.0
|
|
HD11
|
C:LEU68
|
3.7
|
33.3
|
1.0
|
|
HZ2
|
C:LYS16
|
3.7
|
16.8
|
1.0
|
|
HD13
|
C:LEU68
|
4.0
|
33.8
|
1.0
|
|
O
|
C:HOH416
|
4.0
|
24.9
|
1.0
|
|
O
|
C:HOH309
|
4.2
|
27.9
|
1.0
|
|
HD22
|
C:ASN119
|
4.2
|
18.1
|
1.0
|
|
HG21
|
C:THR98
|
4.3
|
22.3
|
0.5
|
|
HE1
|
C:TYR56
|
4.3
|
19.4
|
1.0
|
|
CD1
|
C:LEU68
|
4.3
|
39.5
|
1.0
|
|
HG22
|
C:THR98
|
4.3
|
21.3
|
0.5
|
|
C5'
|
C:IF9201
|
4.4
|
26.4
|
1.0
|
|
HH
|
C:TYR56
|
4.4
|
30.0
|
0.0
|
|
C4
|
C:IF9201
|
4.5
|
20.9
|
1.0
|
|
N3'
|
C:IF9201
|
4.5
|
21.5
|
1.0
|
|
ND2
|
C:ASN119
|
4.5
|
18.4
|
1.0
|
|
HG23
|
C:THR98
|
4.6
|
22.4
|
0.5
|
|
CG2
|
C:THR98
|
4.6
|
22.6
|
0.5
|
|
C5
|
C:IF9201
|
4.6
|
24.1
|
1.0
|
|
H5'
|
C:IF9201
|
4.6
|
27.5
|
1.0
|
|
OD1
|
C:ASN119
|
4.7
|
17.6
|
1.0
|
|
H8
|
C:IF9201
|
4.7
|
24.0
|
1.0
|
|
HD21
|
C:ASN119
|
4.8
|
18.5
|
1.0
|
|
HD12
|
C:LEU68
|
4.8
|
34.4
|
1.0
|
|
CE1
|
C:TYR56
|
4.9
|
17.9
|
1.0
|
|
HD11
|
C:LEU59
|
4.9
|
22.0
|
1.0
|
|
O5'
|
C:IF9201
|
4.9
|
29.3
|
1.0
|
|
H5''
|
C:IF9201
|
4.9
|
28.2
|
1.0
|
|
HB
|
C:THR98
|
4.9
|
18.6
|
0.5
|
|
CG
|
C:ASN119
|
5.0
|
17.2
|
1.0
|
|
CE
|
C:LYS16
|
5.0
|
14.8
|
1.0
|
|
OH
|
C:TYR56
|
5.0
|
23.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F202
b:40.5
occ:1.00
|
F1
|
D:IF9202
|
0.0
|
40.5
|
1.0
|
|
C2'
|
D:IF9202
|
1.4
|
47.8
|
1.0
|
|
H1'
|
D:IF9202
|
2.3
|
40.5
|
1.0
|
|
C1'
|
D:IF9202
|
2.3
|
41.0
|
1.0
|
|
H2
|
D:IF9202
|
2.3
|
42.5
|
1.0
|
|
C1
|
D:IF9202
|
2.4
|
41.8
|
1.0
|
|
C3'
|
D:IF9202
|
2.4
|
52.7
|
1.0
|
|
H4'
|
D:IF9202
|
2.5
|
63.6
|
1.0
|
|
O3'
|
D:IF9202
|
2.7
|
42.1
|
1.0
|
|
C4'
|
D:IF9202
|
2.7
|
77.8
|
1.0
|
|
H1
|
D:IF9202
|
2.8
|
43.3
|
1.0
|
|
O
|
D:HOH305
|
2.8
|
39.8
|
1.0
|
|
HO3'
|
D:IF9202
|
2.9
|
30.0
|
0.0
|
|
O4'
|
D:IF9202
|
2.9
|
44.3
|
1.0
|
|
HZ3
|
D:LYS16
|
3.0
|
18.6
|
1.0
|
|
H3
|
D:IF9202
|
3.1
|
43.4
|
1.0
|
|
H3'
|
D:IF9202
|
3.2
|
53.7
|
1.0
|
|
HZ1
|
D:LYS16
|
3.3
|
18.4
|
1.0
|
|
HD12
|
D:LEU68
|
3.4
|
27.0
|
1.0
|
|
O
|
D:HOH302
|
3.6
|
32.4
|
1.0
|
|
NZ
|
D:LYS16
|
3.6
|
18.6
|
1.0
|
|
N9
|
D:IF9202
|
3.6
|
32.9
|
1.0
|
|
HE1
|
D:TYR56
|
3.7
|
24.6
|
1.0
|
|
HH
|
D:TYR56
|
3.7
|
30.0
|
0.0
|
|
O
|
D:HOH395
|
3.8
|
37.3
|
1.0
|
|
HZ2
|
D:LYS16
|
3.9
|
17.9
|
1.0
|
|
HD23
|
D:LEU68
|
3.9
|
30.7
|
1.0
|
|
O
|
D:HOH390
|
4.0
|
26.6
|
1.0
|
|
HD22
|
D:LEU68
|
4.1
|
31.4
|
1.0
|
|
OH
|
D:TYR56
|
4.2
|
26.5
|
1.0
|
|
CE1
|
D:TYR56
|
4.2
|
26.3
|
1.0
|
|
C5'
|
D:IF9202
|
4.2
|
77.7
|
1.0
|
|
CD1
|
D:LEU68
|
4.2
|
29.2
|
1.0
|
|
HD11
|
D:LEU68
|
4.3
|
26.3
|
1.0
|
|
CD2
|
D:LEU68
|
4.5
|
35.5
|
1.0
|
|
C4
|
D:IF9202
|
4.5
|
34.5
|
1.0
|
|
N3'
|
D:IF9202
|
4.5
|
34.6
|
1.0
|
|
CZ
|
D:TYR56
|
4.5
|
23.8
|
1.0
|
|
H5'
|
D:IF9202
|
4.5
|
78.6
|
1.0
|
|
HD22
|
D:ASN119
|
4.6
|
17.2
|
1.0
|
|
H5''
|
D:IF9202
|
4.6
|
78.7
|
1.0
|
|
C5
|
D:IF9202
|
4.7
|
35.5
|
1.0
|
|
H8
|
D:IF9202
|
4.7
|
36.5
|
1.0
|
|
HE2
|
D:LYS16
|
4.8
|
17.5
|
1.0
|
|
CE
|
D:LYS16
|
4.8
|
16.4
|
1.0
|
|
HD11
|
D:LEU59
|
4.8
|
34.4
|
1.0
|
|
HD13
|
D:LEU68
|
4.9
|
26.4
|
1.0
|
|
HG21
|
D:THR98
|
4.9
|
51.5
|
1.0
|
|
HG22
|
D:THR98
|
4.9
|
49.8
|
1.0
|
|
HD12
|
D:LEU59
|
4.9
|
34.8
|
1.0
|
|
O
|
D:HOH307
|
4.9
|
37.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F201
b:45.3
occ:1.00
|
F1
|
E:IF9201
|
0.0
|
45.3
|
1.0
|
|
C2'
|
E:IF9201
|
1.4
|
51.1
|
1.0
|
|
H1'
|
E:IF9201
|
2.3
|
47.7
|
1.0
|
|
C1'
|
E:IF9201
|
2.3
|
40.7
|
1.0
|
|
C3'
|
E:IF9201
|
2.3
|
62.1
|
1.0
|
|
C1
|
E:IF9201
|
2.5
|
36.5
|
1.0
|
|
H2
|
E:IF9201
|
2.5
|
39.2
|
1.0
|
|
O3'
|
E:IF9201
|
2.7
|
41.6
|
1.0
|
|
H4'
|
E:IF9201
|
2.7
|
70.2
|
1.0
|
|
H1
|
E:IF9201
|
2.8
|
40.4
|
1.0
|
|
C4'
|
E:IF9201
|
2.8
|
72.1
|
1.0
|
|
O
|
E:HOH349
|
2.9
|
30.2
|
1.0
|
|
O4'
|
E:IF9201
|
2.9
|
64.6
|
1.0
|
|
HO3'
|
E:IF9201
|
3.0
|
30.0
|
0.0
|
|
HZ3
|
E:LYS16
|
3.1
|
20.2
|
1.0
|
|
HZ1
|
E:LYS16
|
3.2
|
20.3
|
1.0
|
|
H3'
|
E:IF9201
|
3.2
|
57.7
|
1.0
|
|
H3
|
E:IF9201
|
3.2
|
40.6
|
1.0
|
|
O
|
E:HOH310
|
3.3
|
28.9
|
1.0
|
|
NZ
|
E:LYS16
|
3.5
|
21.7
|
1.0
|
|
O
|
E:HOH421
|
3.6
|
31.1
|
1.0
|
|
HH
|
E:TYR56
|
3.6
|
30.0
|
0.0
|
|
N9
|
E:IF9201
|
3.6
|
49.6
|
1.0
|
|
HE1
|
E:TYR56
|
3.8
|
25.6
|
1.0
|
|
HD11
|
E:LEU68
|
3.8
|
27.3
|
1.0
|
|
HD12
|
E:LEU68
|
3.8
|
28.2
|
1.0
|
|
HZ2
|
E:LYS16
|
3.9
|
19.8
|
1.0
|
|
O
|
E:HOH418
|
4.1
|
31.6
|
1.0
|
|
OH
|
E:TYR56
|
4.2
|
27.6
|
1.0
|
|
HD23
|
E:LEU68
|
4.2
|
36.8
|
1.0
|
|
CE1
|
E:TYR56
|
4.3
|
28.1
|
1.0
|
|
CD1
|
E:LEU68
|
4.3
|
27.8
|
1.0
|
|
C5'
|
E:IF9201
|
4.3
|
87.2
|
1.0
|
|
HD22
|
E:LEU68
|
4.4
|
37.8
|
1.0
|
|
C4
|
E:IF9201
|
4.5
|
39.7
|
1.0
|
|
CZ
|
E:TYR56
|
4.6
|
23.9
|
1.0
|
|
N3'
|
E:IF9201
|
4.6
|
48.1
|
1.0
|
|
C5
|
E:IF9201
|
4.7
|
47.5
|
1.0
|
|
H5'
|
E:IF9201
|
4.7
|
85.7
|
1.0
|
|
H8
|
E:IF9201
|
4.7
|
52.9
|
1.0
|
|
CD2
|
E:LEU68
|
4.7
|
41.6
|
1.0
|
|
HE2
|
E:LYS16
|
4.8
|
16.3
|
1.0
|
|
CE
|
E:LYS16
|
4.8
|
15.7
|
1.0
|
|
H5''
|
E:IF9201
|
4.9
|
86.9
|
1.0
|
|
HD11
|
E:LEU59
|
4.9
|
41.1
|
1.0
|
|
O5'
|
E:IF9201
|
4.9
|
98.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8pyw
Go back to
Fluorine Binding Sites List in 8pyw
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Human Nucleoside-Diphosphate Kinase B Domain Bound to Compound Diphosphate Form of at-9052-Sp.
 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 Bound to Compound Diphosphate Form of at-9052-Sp. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F201
b:43.8
occ:1.00
|
F1
|
F:IF9201
|
0.0
|
43.8
|
1.0
|
|
C2'
|
F:IF9201
|
1.4
|
43.7
|
1.0
|
|
H1'
|
F:IF9201
|
2.3
|
44.6
|
1.0
|
|
C1'
|
F:IF9201
|
2.3
|
43.7
|
1.0
|
|
H2
|
F:IF9201
|
2.3
|
41.4
|
1.0
|
|
C1
|
F:IF9201
|
2.3
|
41.7
|
1.0
|
|
C3'
|
F:IF9201
|
2.4
|
39.0
|
1.0
|
|
H4'
|
F:IF9201
|
2.7
|
57.0
|
1.0
|
|
H1
|
F:IF9201
|
2.8
|
42.4
|
1.0
|
|
C4'
|
F:IF9201
|
2.8
|
58.1
|
1.0
|
|
O4'
|
F:IF9201
|
2.9
|
63.9
|
1.0
|
|
O3'
|
F:IF9201
|
2.9
|
46.8
|
1.0
|
|
HZ3
|
F:LYS16
|
2.9
|
23.2
|
1.0
|
|
HZ1
|
F:LYS16
|
3.0
|
23.2
|
1.0
|
|
H3
|
F:IF9201
|
3.1
|
42.3
|
1.0
|
|
HO3'
|
F:IF9201
|
3.2
|
30.0
|
0.0
|
|
H3'
|
F:IF9201
|
3.3
|
44.9
|
1.0
|
|
NZ
|
F:LYS16
|
3.3
|
24.2
|
1.0
|
|
O
|
F:HOH406
|
3.5
|
45.4
|
1.0
|
|
HD11
|
F:LEU68
|
3.5
|
32.4
|
1.0
|
|
N9
|
F:IF9201
|
3.6
|
35.3
|
1.0
|
|
HZ2
|
F:LYS16
|
3.7
|
22.7
|
1.0
|
|
HH
|
F:TYR56
|
3.7
|
30.0
|
0.0
|
|
HE1
|
F:TYR56
|
3.9
|
24.8
|
1.0
|
|
O
|
F:HOH301
|
4.0
|
40.0
|
1.0
|
|
HD23
|
F:LEU68
|
4.1
|
33.6
|
1.0
|
|
HD12
|
F:LEU68
|
4.1
|
33.1
|
1.0
|
|
CD1
|
F:LEU68
|
4.2
|
33.1
|
1.0
|
|
OH
|
F:TYR56
|
4.2
|
25.4
|
1.0
|
|
HD22
|
F:LEU68
|
4.3
|
34.5
|
1.0
|
|
C5'
|
F:IF9201
|
4.3
|
76.5
|
1.0
|
|
CE1
|
F:TYR56
|
4.4
|
25.8
|
1.0
|
|
C4
|
F:IF9201
|
4.5
|
33.3
|
1.0
|
|
N3'
|
F:IF9201
|
4.5
|
30.9
|
1.0
|
|
CD2
|
F:LEU68
|
4.6
|
34.5
|
1.0
|
|
HE2
|
F:LYS16
|
4.6
|
20.2
|
1.0
|
|
CE
|
F:LYS16
|
4.6
|
19.6
|
1.0
|
|
HD22
|
F:ASN119
|
4.6
|
20.0
|
1.0
|
|
CZ
|
F:TYR56
|
4.6
|
22.7
|
1.0
|
|
C5
|
F:IF9201
|
4.6
|
35.5
|
1.0
|
|
H5'
|
F:IF9201
|
4.7
|
70.0
|
1.0
|
|
H8
|
F:IF9201
|
4.7
|
37.1
|
1.0
|
|
H5''
|
F:IF9201
|
4.8
|
70.7
|
1.0
|
|
HG22
|
F:THR98
|
4.9
|
41.8
|
1.0
|
|
OD1
|
F:ASN119
|
4.9
|
18.9
|
1.0
|
|
HD13
|
F:LEU68
|
4.9
|
32.3
|
1.0
|
|
ND2
|
F:ASN119
|
4.9
|
20.3
|
1.0
|
|
HD11
|
F:LEU59
|
5.0
|
39.2
|
1.0
|
|
HG21
|
F:THR98
|
5.0
|
43.0
|
1.0
|
|
O5'
|
F:IF9201
|
5.0
|
68.5
|
1.0
|
|
Reference:
A.Shannon,
A.Chazot,
M.Feracci,
C.Falcou,
V.Fattorini,
B.Selisko,
S.Good,
A.Moussa,
J.P.Sommadossi,
F.Ferron,
K.Alvarez,
B.Canard.
An Exonuclease-Resistant Chain-Terminating Nucleotide Analogue Targeting the Sars-Cov-2 Replicase Complex. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 38096103
DOI: 10.1093/NAR/GKAD1194
Page generated: Wed Jul 16 06:46:20 2025
|
