Fluorine in PDB 6btw: Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor, PDB code: 6btw
was solved by
R.M.Counago,
C.V.Dos Reis,
G.P.De Souza,
A.Azevedo,
C.Guimaraes,
A.Mascarello,
F.Gama,
M.Ferreira,
K.B.Massirer,
P.Arruda,
A.M.Edwards,
J.M.Elkins,
Structural Genomics Consortium (Sgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.89 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.576,
97.562,
193.284,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
21.5
|
Other elements in 6btw:
The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
(pdb code 6btw). 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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor, PDB code: 6btw:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:46.1
occ:1.00
|
F1
|
A:E8D403
|
0.0
|
46.1
|
1.0
|
C12
|
A:E8D403
|
1.3
|
49.2
|
1.0
|
C13
|
A:E8D403
|
2.3
|
53.0
|
1.0
|
C11
|
A:E8D403
|
2.4
|
52.9
|
1.0
|
O2
|
A:E8D403
|
2.7
|
43.9
|
1.0
|
NZ
|
A:LYS71
|
3.0
|
35.9
|
1.0
|
C15
|
A:E8D403
|
3.4
|
72.7
|
1.0
|
C10
|
A:E8D403
|
3.6
|
51.9
|
1.0
|
C1
|
A:E8D403
|
3.6
|
48.2
|
1.0
|
C14
|
A:E8D403
|
3.9
|
74.3
|
1.0
|
CB
|
A:VAL196
|
3.9
|
21.2
|
1.0
|
CG2
|
A:VAL196
|
4.0
|
22.7
|
1.0
|
C16
|
A:E8D403
|
4.0
|
75.2
|
1.0
|
CE
|
A:LYS71
|
4.1
|
36.0
|
1.0
|
C9
|
A:E8D403
|
4.1
|
49.1
|
1.0
|
N
|
A:ASP197
|
4.1
|
20.5
|
1.0
|
CA
|
A:ASP197
|
4.5
|
22.1
|
1.0
|
OE2
|
A:GLU83
|
4.7
|
23.2
|
1.0
|
CD
|
A:LYS71
|
4.7
|
34.8
|
1.0
|
F2
|
A:E8D403
|
4.7
|
53.7
|
1.0
|
CG1
|
A:VAL196
|
4.7
|
20.8
|
1.0
|
CB
|
A:ASP197
|
4.8
|
24.3
|
1.0
|
N3
|
A:E8D403
|
4.8
|
54.5
|
1.0
|
N1
|
A:E8D403
|
4.8
|
42.6
|
1.0
|
CD1
|
A:ILE51
|
4.9
|
30.1
|
1.0
|
C8
|
A:E8D403
|
4.9
|
68.1
|
1.0
|
C
|
A:VAL196
|
4.9
|
21.8
|
1.0
|
CA
|
A:VAL196
|
5.0
|
20.9
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:53.7
occ:1.00
|
F2
|
A:E8D403
|
0.0
|
53.7
|
1.0
|
C10
|
A:E8D403
|
1.3
|
51.9
|
1.0
|
C9
|
A:E8D403
|
2.3
|
49.1
|
1.0
|
C11
|
A:E8D403
|
2.4
|
52.9
|
1.0
|
O2
|
A:E8D403
|
2.9
|
43.9
|
1.0
|
OH
|
A:TYR87
|
3.0
|
29.9
|
1.0
|
CE
|
A:MET131
|
3.1
|
53.2
|
1.0
|
CB
|
A:PRO111
|
3.3
|
19.1
|
1.0
|
CG
|
A:MET131
|
3.4
|
41.0
|
1.0
|
CB
|
A:MET131
|
3.4
|
31.4
|
1.0
|
CZ
|
A:TYR87
|
3.6
|
28.8
|
1.0
|
C1
|
A:E8D403
|
3.6
|
48.2
|
1.0
|
C12
|
A:E8D403
|
3.6
|
49.2
|
1.0
|
CG
|
A:PRO111
|
3.7
|
19.4
|
1.0
|
SD
|
A:MET131
|
4.0
|
54.3
|
1.0
|
CE2
|
A:TYR87
|
4.1
|
25.5
|
1.0
|
C13
|
A:E8D403
|
4.1
|
53.0
|
1.0
|
CE1
|
A:TYR87
|
4.3
|
30.6
|
1.0
|
CE2
|
A:PHE134
|
4.4
|
25.7
|
1.0
|
O
|
A:ASP132
|
4.6
|
24.3
|
1.0
|
N1
|
A:E8D403
|
4.7
|
42.6
|
1.0
|
F1
|
A:E8D403
|
4.7
|
46.1
|
1.0
|
CA
|
A:MET131
|
4.8
|
26.4
|
1.0
|
CA
|
A:PRO111
|
4.8
|
20.0
|
1.0
|
CG1
|
A:VAL196
|
4.8
|
20.8
|
1.0
|
CD
|
A:PRO111
|
5.0
|
19.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F404
b:44.7
occ:1.00
|
F1
|
B:E8D404
|
0.0
|
44.7
|
1.0
|
C12
|
B:E8D404
|
1.4
|
40.0
|
1.0
|
C13
|
B:E8D404
|
2.4
|
38.6
|
1.0
|
C11
|
B:E8D404
|
2.4
|
37.6
|
1.0
|
O2
|
B:E8D404
|
2.7
|
36.5
|
1.0
|
NZ
|
B:LYS71
|
3.2
|
46.5
|
1.0
|
CE
|
B:LYS71
|
3.3
|
47.6
|
1.0
|
C17
|
B:E8D404
|
3.4
|
49.3
|
1.0
|
C10
|
B:E8D404
|
3.6
|
37.2
|
1.0
|
C1
|
B:E8D404
|
3.6
|
38.2
|
1.0
|
C16
|
B:E8D404
|
3.7
|
48.2
|
1.0
|
O
|
B:HOH656
|
3.8
|
52.3
|
1.0
|
CG2
|
B:VAL196
|
3.8
|
28.6
|
1.0
|
CB
|
B:VAL196
|
4.0
|
26.8
|
1.0
|
C18
|
B:E8D404
|
4.0
|
45.1
|
1.0
|
C9
|
B:E8D404
|
4.1
|
37.7
|
1.0
|
CD1
|
B:ILE51
|
4.2
|
57.6
|
1.0
|
N
|
B:ASP197
|
4.4
|
24.4
|
1.0
|
C15
|
B:E8D404
|
4.6
|
49.4
|
1.0
|
CB
|
B:ASP197
|
4.7
|
28.8
|
1.0
|
CA
|
B:ASP197
|
4.7
|
27.1
|
1.0
|
F2
|
B:E8D404
|
4.7
|
36.2
|
1.0
|
CD
|
B:LYS71
|
4.8
|
46.9
|
1.0
|
CG1
|
B:VAL196
|
4.8
|
26.6
|
1.0
|
N1
|
B:E8D404
|
4.8
|
39.2
|
1.0
|
N3
|
B:E8D404
|
4.8
|
39.5
|
1.0
|
C8
|
B:E8D404
|
4.8
|
46.9
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F404
b:36.2
occ:1.00
|
F2
|
B:E8D404
|
0.0
|
36.2
|
1.0
|
C10
|
B:E8D404
|
1.3
|
37.2
|
1.0
|
C9
|
B:E8D404
|
2.3
|
37.7
|
1.0
|
C11
|
B:E8D404
|
2.4
|
37.6
|
1.0
|
O2
|
B:E8D404
|
2.8
|
36.5
|
1.0
|
O
|
B:HOH509
|
3.1
|
40.0
|
1.0
|
CE
|
B:MET131
|
3.4
|
29.4
|
1.0
|
CB
|
B:PRO111
|
3.5
|
25.7
|
1.0
|
CB
|
B:MET131
|
3.5
|
31.9
|
1.0
|
C12
|
B:E8D404
|
3.6
|
40.0
|
1.0
|
C1
|
B:E8D404
|
3.6
|
38.2
|
1.0
|
CG
|
B:PRO111
|
3.7
|
24.9
|
1.0
|
CG
|
B:MET131
|
3.7
|
30.0
|
1.0
|
OH
|
B:TYR87
|
4.0
|
23.7
|
1.0
|
CE2
|
B:PHE134
|
4.1
|
29.2
|
1.0
|
C13
|
B:E8D404
|
4.1
|
38.6
|
1.0
|
SD
|
B:MET131
|
4.3
|
29.9
|
1.0
|
CG1
|
B:VAL196
|
4.5
|
26.6
|
1.0
|
CB
|
B:VAL196
|
4.6
|
26.8
|
1.0
|
O
|
B:ASP132
|
4.7
|
33.7
|
1.0
|
F1
|
B:E8D404
|
4.7
|
44.7
|
1.0
|
N1
|
B:E8D404
|
4.7
|
39.2
|
1.0
|
NZ
|
B:LYS71
|
4.8
|
46.5
|
1.0
|
CA
|
B:MET131
|
4.8
|
32.4
|
1.0
|
CE
|
B:LYS71
|
4.9
|
47.6
|
1.0
|
CZ
|
B:TYR87
|
4.9
|
25.4
|
1.0
|
CD2
|
B:PHE134
|
4.9
|
30.4
|
1.0
|
CZ
|
B:PHE134
|
4.9
|
28.4
|
1.0
|
CD
|
B:PRO111
|
5.0
|
25.9
|
1.0
|
CA
|
B:PRO111
|
5.0
|
25.3
|
1.0
|
N
|
B:ASP132
|
5.0
|
31.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F404
b:26.1
occ:1.00
|
F1
|
D:E8D404
|
0.0
|
26.1
|
1.0
|
C12
|
D:E8D404
|
1.3
|
24.1
|
1.0
|
C13
|
D:E8D404
|
2.3
|
26.0
|
1.0
|
C11
|
D:E8D404
|
2.4
|
24.4
|
1.0
|
O2
|
D:E8D404
|
2.8
|
25.9
|
1.0
|
O
|
D:HOH508
|
3.2
|
29.2
|
1.0
|
CB
|
D:MET131
|
3.4
|
28.2
|
1.0
|
CE
|
D:MET131
|
3.4
|
26.4
|
1.0
|
CG
|
D:MET131
|
3.6
|
27.6
|
1.0
|
CB
|
D:PRO111
|
3.6
|
20.6
|
1.0
|
C1
|
D:E8D404
|
3.6
|
28.2
|
1.0
|
C10
|
D:E8D404
|
3.6
|
27.8
|
1.0
|
CG
|
D:PRO111
|
3.6
|
20.4
|
1.0
|
OH
|
D:TYR87
|
4.0
|
25.3
|
1.0
|
C9
|
D:E8D404
|
4.1
|
26.4
|
1.0
|
CE2
|
D:PHE134
|
4.2
|
24.8
|
1.0
|
CG1
|
D:VAL196
|
4.2
|
21.6
|
1.0
|
SD
|
D:MET131
|
4.3
|
26.3
|
1.0
|
CB
|
D:VAL196
|
4.4
|
20.2
|
1.0
|
O
|
D:ASP132
|
4.6
|
26.7
|
1.0
|
N1
|
D:E8D404
|
4.7
|
32.0
|
1.0
|
F2
|
D:E8D404
|
4.7
|
31.3
|
1.0
|
CA
|
D:MET131
|
4.8
|
29.9
|
1.0
|
CD2
|
D:PHE134
|
4.9
|
27.9
|
1.0
|
CZ
|
D:TYR87
|
4.9
|
23.5
|
1.0
|
CD
|
D:LYS71
|
4.9
|
37.1
|
1.0
|
NZ
|
D:LYS71
|
5.0
|
35.1
|
1.0
|
N
|
D:ASP132
|
5.0
|
29.7
|
1.0
|
CD
|
D:PRO111
|
5.0
|
20.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6btw
Go back to
Fluorine Binding Sites List in 6btw
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor
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 Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F404
b:31.3
occ:1.00
|
F2
|
D:E8D404
|
0.0
|
31.3
|
1.0
|
C10
|
D:E8D404
|
1.4
|
27.8
|
1.0
|
C9
|
D:E8D404
|
2.4
|
26.4
|
1.0
|
C11
|
D:E8D404
|
2.4
|
24.4
|
1.0
|
O2
|
D:E8D404
|
2.7
|
25.9
|
1.0
|
NZ
|
D:LYS71
|
3.3
|
35.1
|
1.0
|
C17
|
D:E8D404
|
3.4
|
47.4
|
1.0
|
O
|
D:HOH681
|
3.4
|
44.1
|
1.0
|
C12
|
D:E8D404
|
3.6
|
24.1
|
1.0
|
C1
|
D:E8D404
|
3.6
|
28.2
|
1.0
|
CE
|
D:LYS71
|
3.6
|
36.7
|
1.0
|
CD1
|
D:ILE51
|
3.7
|
52.5
|
1.0
|
C16
|
D:E8D404
|
3.7
|
48.7
|
1.0
|
CG2
|
D:VAL196
|
3.9
|
20.3
|
1.0
|
C18
|
D:E8D404
|
4.0
|
45.6
|
1.0
|
C13
|
D:E8D404
|
4.1
|
26.0
|
1.0
|
CD
|
D:LYS71
|
4.1
|
37.1
|
1.0
|
CB
|
D:VAL196
|
4.2
|
20.2
|
1.0
|
O
|
D:HOH503
|
4.2
|
44.7
|
1.0
|
C15
|
D:E8D404
|
4.5
|
50.8
|
1.0
|
N
|
D:ASP197
|
4.5
|
21.7
|
1.0
|
F1
|
D:E8D404
|
4.7
|
26.1
|
1.0
|
CB
|
D:ASP197
|
4.8
|
26.0
|
1.0
|
C8
|
D:E8D404
|
4.8
|
45.1
|
1.0
|
N3
|
D:E8D404
|
4.8
|
35.5
|
1.0
|
N1
|
D:E8D404
|
4.8
|
32.0
|
1.0
|
CA
|
D:ASP197
|
4.9
|
23.3
|
1.0
|
CG
|
D:LYS71
|
4.9
|
38.1
|
1.0
|
C14
|
D:E8D404
|
5.0
|
48.8
|
1.0
|
CG1
|
D:VAL196
|
5.0
|
21.6
|
1.0
|
|
Reference:
R.M.Counago,
C.V.Dos Reis,
G.P.De Souza,
H.Azevedo,
C.Guimaraes,
A.Mascarello,
F.Gama,
M.Ferreira,
K.B.Massirer,
P.Arruda,
A.M.Edwards,
J.M.Elkins,
Structural Genomics Consortium (Sgc).
Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Phenyl-Pteridinone Inhibitor To Be Published.
Page generated: Thu Aug 1 18:21:44 2024
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