Fluorine in PDB 6vxu: Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Enzymatic activity of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
All present enzymatic activity of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471:
2.7.11.1;
Protein crystallography data
The structure of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471, PDB code: 6vxu
was solved by
C.V.Dos Reis,
L.A.Dutra,
F.H.Gama,
A.Mascarello,
H.Azevedo,
C.R.Guimaraes,
K.B.Massirer,
P.Arruda,
A.M.Edwards,
R.M.Counago,
Structural Genomicsconsortium (Sgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.771,
96.3,
191.988,
90,
90,
90
|
R / Rfree (%)
|
18.4 /
20.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
(pdb code 6vxu). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471, PDB code: 6vxu:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 1 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:44.0
occ:1.00
|
F1
|
A:RTJ401
|
0.0
|
44.0
|
1.0
|
C6
|
A:RTJ401
|
1.3
|
45.8
|
1.0
|
C1
|
A:RTJ401
|
2.3
|
46.2
|
1.0
|
C5
|
A:RTJ401
|
2.4
|
44.9
|
1.0
|
O2
|
A:RTJ401
|
2.7
|
42.5
|
1.0
|
CB
|
A:MET131
|
3.2
|
33.1
|
1.0
|
CB
|
A:PRO111
|
3.3
|
30.1
|
1.0
|
CE
|
A:MET131
|
3.3
|
37.7
|
1.0
|
OH
|
A:TYR87
|
3.3
|
34.3
|
1.0
|
CG
|
A:MET131
|
3.4
|
35.1
|
1.0
|
C4
|
A:RTJ401
|
3.6
|
49.8
|
1.0
|
C2
|
A:RTJ401
|
3.6
|
48.7
|
1.0
|
CG
|
A:PRO111
|
3.7
|
29.8
|
1.0
|
CZ
|
A:TYR87
|
3.8
|
33.7
|
1.0
|
CE2
|
A:TYR87
|
4.1
|
33.6
|
1.0
|
C3
|
A:RTJ401
|
4.1
|
49.1
|
1.0
|
SD
|
A:MET131
|
4.1
|
38.3
|
1.0
|
CE2
|
A:PHE134
|
4.3
|
32.7
|
1.0
|
CE1
|
A:TYR87
|
4.6
|
34.1
|
1.0
|
CA
|
A:MET131
|
4.6
|
30.6
|
1.0
|
F2
|
A:RTJ401
|
4.7
|
39.2
|
1.0
|
O
|
A:ASP132
|
4.7
|
31.1
|
1.0
|
CA
|
A:PRO111
|
4.7
|
31.1
|
1.0
|
N
|
A:ASP132
|
4.7
|
30.8
|
1.0
|
N1
|
A:RTJ401
|
4.8
|
44.8
|
1.0
|
CG1
|
A:VAL196
|
4.8
|
33.2
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 2 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:39.2
occ:1.00
|
F2
|
A:RTJ401
|
0.0
|
39.2
|
1.0
|
C4
|
A:RTJ401
|
1.3
|
49.8
|
1.0
|
C3
|
A:RTJ401
|
2.3
|
49.1
|
1.0
|
C5
|
A:RTJ401
|
2.3
|
44.9
|
1.0
|
O
|
A:HOH501
|
2.6
|
50.2
|
1.0
|
O2
|
A:RTJ401
|
2.7
|
42.5
|
1.0
|
NZ
|
A:LYS71
|
3.4
|
45.4
|
1.0
|
C20
|
A:RTJ401
|
3.5
|
44.8
|
1.0
|
C6
|
A:RTJ401
|
3.6
|
45.8
|
1.0
|
C2
|
A:RTJ401
|
3.6
|
48.7
|
1.0
|
CD
|
A:LYS71
|
3.9
|
41.5
|
1.0
|
C18
|
A:RTJ401
|
4.0
|
44.7
|
1.0
|
CE
|
A:LYS71
|
4.1
|
43.5
|
1.0
|
C1
|
A:RTJ401
|
4.1
|
46.2
|
1.0
|
CD1
|
A:ILE51
|
4.4
|
37.1
|
1.0
|
CB
|
A:VAL196
|
4.4
|
32.6
|
1.0
|
CG2
|
A:VAL196
|
4.6
|
32.7
|
1.0
|
N3
|
A:RTJ401
|
4.7
|
43.6
|
1.0
|
C17
|
A:RTJ401
|
4.7
|
41.8
|
1.0
|
F1
|
A:RTJ401
|
4.7
|
44.0
|
1.0
|
N1
|
A:RTJ401
|
4.8
|
44.8
|
1.0
|
N
|
A:ASP197
|
4.8
|
33.6
|
1.0
|
C19
|
A:RTJ401
|
4.9
|
46.0
|
1.0
|
CG
|
A:LYS71
|
5.0
|
39.7
|
1.0
|
CG1
|
A:VAL196
|
5.0
|
33.2
|
1.0
|
OE2
|
A:GLU83
|
5.0
|
34.2
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 3 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:52.5
occ:1.00
|
F1
|
B:RTJ401
|
0.0
|
52.5
|
1.0
|
C6
|
B:RTJ401
|
1.3
|
59.8
|
1.0
|
C1
|
B:RTJ401
|
2.3
|
59.3
|
1.0
|
C5
|
B:RTJ401
|
2.3
|
60.3
|
1.0
|
O2
|
B:RTJ401
|
2.7
|
45.4
|
1.0
|
NZ
|
B:LYS71
|
3.4
|
53.1
|
1.0
|
C4
|
B:RTJ401
|
3.6
|
67.4
|
1.0
|
C2
|
B:RTJ401
|
3.6
|
62.8
|
1.0
|
CD1
|
B:ILE51
|
3.6
|
66.0
|
1.0
|
CE
|
B:LYS71
|
3.7
|
55.2
|
1.0
|
C19
|
B:RTJ401
|
4.1
|
59.4
|
1.0
|
C3
|
B:RTJ401
|
4.1
|
65.3
|
1.0
|
CD
|
B:LYS71
|
4.2
|
55.4
|
1.0
|
C20
|
B:RTJ401
|
4.2
|
58.6
|
1.0
|
CG2
|
B:VAL196
|
4.3
|
40.6
|
1.0
|
CB
|
B:VAL196
|
4.4
|
40.7
|
1.0
|
C17
|
B:RTJ401
|
4.5
|
56.1
|
1.0
|
N
|
B:ASP197
|
4.6
|
41.3
|
1.0
|
N3
|
B:RTJ401
|
4.6
|
56.3
|
1.0
|
F2
|
B:RTJ401
|
4.7
|
45.7
|
1.0
|
C18
|
B:RTJ401
|
4.7
|
59.5
|
1.0
|
N1
|
B:RTJ401
|
4.8
|
59.9
|
1.0
|
CG
|
B:LYS71
|
4.9
|
57.3
|
1.0
|
CG1
|
B:ILE51
|
4.9
|
67.4
|
1.0
|
CA
|
B:ASP197
|
4.9
|
42.9
|
1.0
|
CB
|
B:ASP197
|
5.0
|
44.6
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 4 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:45.7
occ:1.00
|
F2
|
B:RTJ401
|
0.0
|
45.7
|
1.0
|
C4
|
B:RTJ401
|
1.4
|
67.4
|
1.0
|
C3
|
B:RTJ401
|
2.4
|
65.3
|
1.0
|
C5
|
B:RTJ401
|
2.4
|
60.3
|
1.0
|
O2
|
B:RTJ401
|
2.7
|
45.4
|
1.0
|
O
|
B:HOH501
|
3.3
|
43.7
|
1.0
|
CB
|
B:MET131
|
3.3
|
47.2
|
1.0
|
CG
|
B:MET131
|
3.5
|
47.1
|
1.0
|
CE
|
B:MET131
|
3.6
|
44.3
|
1.0
|
C6
|
B:RTJ401
|
3.6
|
59.8
|
1.0
|
C2
|
B:RTJ401
|
3.6
|
62.8
|
1.0
|
CB
|
B:PRO111
|
3.7
|
40.4
|
1.0
|
CG
|
B:PRO111
|
3.8
|
38.8
|
1.0
|
OH
|
B:TYR87
|
4.1
|
40.7
|
1.0
|
C1
|
B:RTJ401
|
4.1
|
59.3
|
1.0
|
CE2
|
B:PHE134
|
4.3
|
42.9
|
1.0
|
SD
|
B:MET131
|
4.3
|
47.1
|
1.0
|
CG1
|
B:VAL196
|
4.5
|
41.1
|
1.0
|
O
|
B:ASP132
|
4.5
|
48.4
|
1.0
|
CB
|
B:VAL196
|
4.5
|
40.7
|
1.0
|
F1
|
B:RTJ401
|
4.7
|
52.5
|
1.0
|
N1
|
B:RTJ401
|
4.8
|
59.9
|
1.0
|
CA
|
B:MET131
|
4.8
|
48.8
|
1.0
|
N
|
B:ASP132
|
4.9
|
47.7
|
1.0
|
CD
|
B:LYS71
|
4.9
|
55.4
|
1.0
|
CZ
|
B:TYR87
|
5.0
|
40.9
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 5 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:58.1
occ:1.00
|
F1
|
C:VBD401
|
0.0
|
58.1
|
1.0
|
C6
|
C:VBD401
|
1.4
|
61.4
|
1.0
|
C1
|
C:VBD401
|
2.3
|
61.9
|
1.0
|
C5
|
C:VBD401
|
2.4
|
62.0
|
1.0
|
O2
|
C:VBD401
|
2.7
|
56.1
|
1.0
|
OH
|
C:TYR87
|
3.0
|
38.5
|
1.0
|
CB
|
C:MET131
|
3.3
|
39.6
|
1.0
|
CE
|
C:MET131
|
3.4
|
49.2
|
1.0
|
CG
|
C:MET131
|
3.4
|
43.3
|
1.0
|
CZ
|
C:TYR87
|
3.5
|
37.3
|
1.0
|
CB
|
C:PRO111
|
3.5
|
31.5
|
1.0
|
C4
|
C:VBD401
|
3.6
|
65.9
|
1.0
|
C2
|
C:VBD401
|
3.6
|
64.7
|
1.0
|
CE2
|
C:TYR87
|
3.9
|
35.5
|
1.0
|
CG
|
C:PRO111
|
3.9
|
31.0
|
1.0
|
SD
|
C:MET131
|
4.1
|
48.4
|
1.0
|
C3
|
C:VBD401
|
4.1
|
64.7
|
1.0
|
CE1
|
C:TYR87
|
4.2
|
37.0
|
1.0
|
O
|
C:ASP132
|
4.5
|
36.1
|
1.0
|
CE2
|
C:PHE134
|
4.6
|
36.4
|
1.0
|
CA
|
C:MET131
|
4.7
|
37.0
|
1.0
|
F2
|
C:VBD401
|
4.7
|
52.3
|
1.0
|
N1
|
C:VBD401
|
4.8
|
62.5
|
1.0
|
N
|
C:ASP132
|
4.9
|
34.6
|
1.0
|
CD2
|
C:TYR87
|
4.9
|
35.0
|
1.0
|
CG1
|
C:VAL196
|
4.9
|
33.8
|
1.0
|
CA
|
C:PRO111
|
5.0
|
31.2
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 6 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:52.3
occ:1.00
|
F2
|
C:VBD401
|
0.0
|
52.3
|
1.0
|
C4
|
C:VBD401
|
1.3
|
65.9
|
1.0
|
C3
|
C:VBD401
|
2.3
|
64.7
|
1.0
|
C5
|
C:VBD401
|
2.4
|
62.0
|
1.0
|
O2
|
C:VBD401
|
2.7
|
56.1
|
1.0
|
C20
|
C:VBD401
|
3.1
|
60.8
|
1.0
|
NZ
|
C:LYS71
|
3.2
|
45.0
|
1.0
|
C6
|
C:VBD401
|
3.6
|
61.4
|
1.0
|
C2
|
C:VBD401
|
3.6
|
64.7
|
1.0
|
C18
|
C:VBD401
|
3.7
|
59.1
|
1.0
|
CB
|
C:VAL196
|
4.1
|
33.2
|
1.0
|
C1
|
C:VBD401
|
4.1
|
61.9
|
1.0
|
CE
|
C:LYS71
|
4.2
|
44.3
|
1.0
|
CG2
|
C:VAL196
|
4.2
|
33.7
|
1.0
|
CD
|
C:LYS71
|
4.3
|
44.0
|
1.0
|
C19
|
C:VBD401
|
4.4
|
61.7
|
1.0
|
N
|
C:ASP197
|
4.5
|
34.4
|
1.0
|
C17
|
C:VBD401
|
4.6
|
56.5
|
1.0
|
N3
|
C:VBD401
|
4.6
|
57.5
|
1.0
|
CG1
|
C:VAL196
|
4.7
|
33.8
|
1.0
|
F1
|
C:VBD401
|
4.7
|
58.1
|
1.0
|
N1
|
C:VBD401
|
4.8
|
62.5
|
1.0
|
OE2
|
C:GLU83
|
4.8
|
36.4
|
1.0
|
CA
|
C:ASP197
|
4.9
|
35.4
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 7 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F401
b:44.4
occ:1.00
|
F1
|
D:RTJ401
|
0.0
|
44.4
|
1.0
|
C6
|
D:RTJ401
|
1.3
|
50.8
|
1.0
|
C1
|
D:RTJ401
|
2.3
|
51.8
|
1.0
|
C5
|
D:RTJ401
|
2.3
|
49.6
|
1.0
|
O2
|
D:RTJ401
|
2.7
|
38.6
|
1.0
|
C20
|
D:RTJ401
|
3.2
|
45.2
|
1.0
|
NZ
|
D:LYS71
|
3.2
|
43.1
|
1.0
|
CE
|
D:LYS71
|
3.6
|
44.6
|
1.0
|
C4
|
D:RTJ401
|
3.6
|
51.0
|
1.0
|
C2
|
D:RTJ401
|
3.6
|
48.6
|
1.0
|
C18
|
D:RTJ401
|
3.6
|
45.3
|
1.0
|
CD1
|
D:ILE51
|
3.8
|
56.9
|
1.0
|
CD
|
D:LYS71
|
4.0
|
44.8
|
1.0
|
CG2
|
D:VAL196
|
4.0
|
33.5
|
1.0
|
C3
|
D:RTJ401
|
4.1
|
50.0
|
1.0
|
O
|
D:HOH534
|
4.1
|
56.2
|
1.0
|
CB
|
D:VAL196
|
4.3
|
33.0
|
1.0
|
C19
|
D:RTJ401
|
4.3
|
45.9
|
1.0
|
N3
|
D:RTJ401
|
4.6
|
43.5
|
1.0
|
C17
|
D:RTJ401
|
4.6
|
42.9
|
1.0
|
F2
|
D:RTJ401
|
4.7
|
37.1
|
1.0
|
CG
|
D:LYS71
|
4.7
|
45.9
|
1.0
|
N1
|
D:RTJ401
|
4.7
|
47.7
|
1.0
|
N
|
D:ASP197
|
4.8
|
32.9
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6vxu
Go back to
Fluorine Binding Sites List in 6vxu
Fluorine binding site 8 out
of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F401
b:37.1
occ:1.00
|
F2
|
D:RTJ401
|
0.0
|
37.1
|
1.0
|
C4
|
D:RTJ401
|
1.3
|
51.0
|
1.0
|
C3
|
D:RTJ401
|
2.3
|
50.0
|
1.0
|
C5
|
D:RTJ401
|
2.3
|
49.6
|
1.0
|
O2
|
D:RTJ401
|
2.7
|
38.6
|
1.0
|
O
|
D:HOH514
|
3.3
|
38.0
|
1.0
|
CE
|
D:MET131
|
3.4
|
33.6
|
1.0
|
CB
|
D:MET131
|
3.4
|
36.1
|
1.0
|
CG
|
D:PRO111
|
3.6
|
30.2
|
1.0
|
C6
|
D:RTJ401
|
3.6
|
50.8
|
1.0
|
C2
|
D:RTJ401
|
3.6
|
48.6
|
1.0
|
CG
|
D:MET131
|
3.6
|
36.0
|
1.0
|
CB
|
D:PRO111
|
3.6
|
31.6
|
1.0
|
OH
|
D:TYR87
|
3.9
|
31.7
|
1.0
|
C1
|
D:RTJ401
|
4.1
|
51.8
|
1.0
|
CG1
|
D:VAL196
|
4.2
|
33.6
|
1.0
|
CE2
|
D:PHE134
|
4.2
|
36.0
|
1.0
|
SD
|
D:MET131
|
4.3
|
35.2
|
1.0
|
CB
|
D:VAL196
|
4.4
|
33.0
|
1.0
|
O
|
D:ASP132
|
4.7
|
37.9
|
1.0
|
F1
|
D:RTJ401
|
4.7
|
44.4
|
1.0
|
N1
|
D:RTJ401
|
4.7
|
47.7
|
1.0
|
CZ
|
D:TYR87
|
4.8
|
31.9
|
1.0
|
CA
|
D:MET131
|
4.9
|
37.3
|
1.0
|
CD
|
D:PRO111
|
4.9
|
29.5
|
1.0
|
CD
|
D:LYS71
|
4.9
|
44.8
|
1.0
|
|
Reference:
C.R.Guimaraes,
R.M.Counago.
Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 To Be Published.
Page generated: Fri Aug 2 03:16:48 2024
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