Fluorine in PDB 6cfm: Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-Pteridinone Inhibitor
Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-Pteridinone Inhibitor
All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-Pteridinone Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-Pteridinone Inhibitor, PDB code: 6cfm
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)
|
20.00 /
2.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.618,
96.839,
192.318,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.1 /
24.5
|
Other elements in 6cfm:
The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor
(pdb code 6cfm). 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 Propynyl-Pteridinone Inhibitor, PDB code: 6cfm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:47.9
occ:1.00
|
F1
|
A:EA7402
|
0.0
|
47.9
|
1.0
|
C11
|
A:EA7402
|
1.4
|
48.6
|
1.0
|
C12
|
A:EA7402
|
2.3
|
47.4
|
1.0
|
C10
|
A:EA7402
|
2.4
|
48.8
|
1.0
|
O2
|
A:EA7402
|
2.8
|
47.4
|
1.0
|
OH
|
A:TYR87
|
3.0
|
34.2
|
1.0
|
CE
|
A:MET131
|
3.3
|
51.9
|
1.0
|
CG
|
A:MET131
|
3.5
|
46.6
|
1.0
|
CB
|
A:MET131
|
3.5
|
41.6
|
1.0
|
CZ
|
A:TYR87
|
3.5
|
32.2
|
1.0
|
CB
|
A:PRO111
|
3.6
|
30.9
|
1.0
|
C7
|
A:EA7402
|
3.6
|
46.6
|
1.0
|
C9
|
A:EA7402
|
3.6
|
47.0
|
1.0
|
CG
|
A:PRO111
|
3.8
|
30.5
|
1.0
|
CE2
|
A:TYR87
|
4.1
|
31.8
|
1.0
|
SD
|
A:MET131
|
4.1
|
55.1
|
1.0
|
C8
|
A:EA7402
|
4.1
|
47.1
|
1.0
|
CE1
|
A:TYR87
|
4.2
|
32.3
|
1.0
|
CE2
|
A:PHE134
|
4.6
|
30.3
|
1.0
|
O
|
A:ASP132
|
4.6
|
31.9
|
1.0
|
F2
|
A:EA7402
|
4.7
|
47.9
|
1.0
|
N5
|
A:EA7402
|
4.7
|
45.2
|
1.0
|
CA
|
A:MET131
|
4.8
|
36.3
|
1.0
|
CG1
|
A:VAL196
|
4.9
|
27.7
|
1.0
|
CB
|
A:VAL196
|
4.9
|
28.2
|
1.0
|
N
|
A:ASP132
|
5.0
|
33.1
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:47.9
occ:1.00
|
F2
|
A:EA7402
|
0.0
|
47.9
|
1.0
|
C9
|
A:EA7402
|
1.4
|
47.0
|
1.0
|
C10
|
A:EA7402
|
2.4
|
48.8
|
1.0
|
C8
|
A:EA7402
|
2.4
|
47.1
|
1.0
|
O2
|
A:EA7402
|
2.7
|
47.4
|
1.0
|
NZ
|
A:LYS71
|
3.1
|
44.2
|
1.0
|
C11
|
A:EA7402
|
3.6
|
48.6
|
1.0
|
C7
|
A:EA7402
|
3.6
|
46.6
|
1.0
|
CG2
|
A:VAL196
|
3.9
|
28.5
|
1.0
|
CB
|
A:VAL196
|
4.0
|
28.2
|
1.0
|
C12
|
A:EA7402
|
4.1
|
47.4
|
1.0
|
N
|
A:ASP197
|
4.2
|
30.1
|
1.0
|
CE
|
A:LYS71
|
4.3
|
43.2
|
1.0
|
CA
|
A:ASP197
|
4.5
|
31.0
|
1.0
|
F1
|
A:EA7402
|
4.7
|
47.9
|
1.0
|
OE2
|
A:GLU83
|
4.7
|
33.6
|
1.0
|
CD
|
A:LYS71
|
4.8
|
42.6
|
1.0
|
CB
|
A:ASP197
|
4.8
|
33.4
|
1.0
|
CD1
|
A:ILE51
|
4.8
|
37.4
|
1.0
|
C17
|
A:EA7402
|
4.8
|
45.8
|
1.0
|
N5
|
A:EA7402
|
4.8
|
45.2
|
1.0
|
N3
|
A:EA7402
|
4.8
|
46.9
|
1.0
|
CG1
|
A:VAL196
|
4.9
|
27.7
|
1.0
|
C
|
A:VAL196
|
5.0
|
28.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F404
b:48.4
occ:1.00
|
F1
|
B:EA7404
|
0.0
|
48.4
|
1.0
|
C11
|
B:EA7404
|
1.4
|
46.8
|
1.0
|
C10
|
B:EA7404
|
2.4
|
47.1
|
1.0
|
C12
|
B:EA7404
|
2.4
|
46.5
|
1.0
|
O2
|
B:EA7404
|
2.7
|
45.3
|
1.0
|
CE
|
B:MET131
|
3.4
|
55.7
|
1.0
|
CB
|
B:MET131
|
3.5
|
53.9
|
1.0
|
CG
|
B:MET131
|
3.6
|
54.8
|
1.0
|
C9
|
B:EA7404
|
3.6
|
47.9
|
1.0
|
C7
|
B:EA7404
|
3.6
|
47.5
|
1.0
|
CB
|
B:PRO111
|
3.7
|
48.6
|
1.0
|
CG
|
B:PRO111
|
3.8
|
48.5
|
1.0
|
OH
|
B:TYR87
|
3.9
|
45.7
|
1.0
|
C8
|
B:EA7404
|
4.1
|
46.9
|
1.0
|
SD
|
B:MET131
|
4.2
|
57.4
|
1.0
|
CG1
|
B:VAL196
|
4.3
|
41.8
|
1.0
|
CB
|
B:VAL196
|
4.4
|
41.4
|
1.0
|
CE2
|
B:PHE134
|
4.5
|
38.3
|
1.0
|
F2
|
B:EA7404
|
4.7
|
43.2
|
1.0
|
CD
|
B:LYS71
|
4.7
|
65.1
|
1.0
|
N5
|
B:EA7404
|
4.7
|
49.2
|
1.0
|
CZ
|
B:TYR87
|
4.8
|
42.2
|
1.0
|
NZ
|
B:LYS71
|
4.9
|
64.0
|
1.0
|
CA
|
B:MET131
|
4.9
|
52.3
|
1.0
|
O
|
B:ASP132
|
5.0
|
58.9
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F404
b:43.2
occ:1.00
|
F2
|
B:EA7404
|
0.0
|
43.2
|
1.0
|
C9
|
B:EA7404
|
1.4
|
47.9
|
1.0
|
C8
|
B:EA7404
|
2.4
|
46.9
|
1.0
|
C10
|
B:EA7404
|
2.4
|
47.1
|
1.0
|
O2
|
B:EA7404
|
2.8
|
45.3
|
1.0
|
NZ
|
B:LYS71
|
3.4
|
64.0
|
1.0
|
C11
|
B:EA7404
|
3.6
|
46.8
|
1.0
|
C7
|
B:EA7404
|
3.6
|
47.5
|
1.0
|
CE
|
B:LYS71
|
3.8
|
65.2
|
1.0
|
CG2
|
B:VAL196
|
4.0
|
41.6
|
1.0
|
CD1
|
B:ILE51
|
4.0
|
75.8
|
1.0
|
C12
|
B:EA7404
|
4.1
|
46.5
|
1.0
|
CB
|
B:VAL196
|
4.1
|
41.4
|
1.0
|
N
|
B:ASP197
|
4.4
|
39.8
|
1.0
|
CD
|
B:LYS71
|
4.4
|
65.1
|
1.0
|
CB
|
B:ASP197
|
4.5
|
41.8
|
1.0
|
CA
|
B:ASP197
|
4.7
|
41.0
|
1.0
|
F1
|
B:EA7404
|
4.7
|
48.4
|
1.0
|
N5
|
B:EA7404
|
4.9
|
49.2
|
1.0
|
N3
|
B:EA7404
|
4.9
|
52.2
|
1.0
|
CG1
|
B:VAL196
|
5.0
|
41.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F404
b:32.0
occ:1.00
|
F1
|
D:EA7404
|
0.0
|
32.0
|
1.0
|
C11
|
D:EA7404
|
1.3
|
29.8
|
1.0
|
C12
|
D:EA7404
|
2.3
|
29.7
|
1.0
|
C10
|
D:EA7404
|
2.3
|
29.7
|
1.0
|
O2
|
D:EA7404
|
2.7
|
28.9
|
1.0
|
CE
|
D:MET131
|
3.3
|
44.3
|
1.0
|
CG
|
D:MET131
|
3.4
|
40.2
|
1.0
|
CB
|
D:MET131
|
3.4
|
38.9
|
1.0
|
C9
|
D:EA7404
|
3.6
|
30.8
|
1.0
|
C7
|
D:EA7404
|
3.6
|
30.6
|
1.0
|
CG
|
D:PRO111
|
3.7
|
32.8
|
1.0
|
CB
|
D:PRO111
|
3.7
|
32.8
|
1.0
|
OH
|
D:TYR87
|
3.7
|
34.1
|
1.0
|
SD
|
D:MET131
|
4.0
|
43.0
|
1.0
|
C8
|
D:EA7404
|
4.1
|
30.3
|
1.0
|
CB
|
D:VAL196
|
4.3
|
27.6
|
1.0
|
CG1
|
D:VAL196
|
4.4
|
27.9
|
1.0
|
CE2
|
D:PHE134
|
4.5
|
35.2
|
1.0
|
CZ
|
D:TYR87
|
4.6
|
33.8
|
1.0
|
F2
|
D:EA7404
|
4.7
|
33.1
|
1.0
|
N5
|
D:EA7404
|
4.7
|
30.9
|
1.0
|
CA
|
D:MET131
|
4.8
|
38.8
|
1.0
|
CD
|
D:LYS71
|
4.9
|
51.0
|
1.0
|
NZ
|
D:LYS71
|
4.9
|
52.9
|
1.0
|
CD
|
D:PRO111
|
4.9
|
33.1
|
1.0
|
OE2
|
D:GLU83
|
4.9
|
40.8
|
1.0
|
O
|
D:ASP132
|
5.0
|
39.5
|
1.0
|
CA
|
D:VAL196
|
5.0
|
28.2
|
1.0
|
N
|
D:ASP197
|
5.0
|
29.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6cfm
Go back to
Fluorine Binding Sites List in 6cfm
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Propynyl-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 Propynyl-Pteridinone Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F404
b:33.1
occ:1.00
|
F2
|
D:EA7404
|
0.0
|
33.1
|
1.0
|
C9
|
D:EA7404
|
1.3
|
30.8
|
1.0
|
C8
|
D:EA7404
|
2.3
|
30.3
|
1.0
|
C10
|
D:EA7404
|
2.3
|
29.7
|
1.0
|
O2
|
D:EA7404
|
2.7
|
28.9
|
1.0
|
NZ
|
D:LYS71
|
3.4
|
52.9
|
1.0
|
C11
|
D:EA7404
|
3.6
|
29.8
|
1.0
|
C7
|
D:EA7404
|
3.6
|
30.6
|
1.0
|
CG2
|
D:VAL196
|
3.7
|
27.9
|
1.0
|
O
|
D:HOH535
|
3.8
|
37.1
|
1.0
|
CE
|
D:LYS71
|
3.9
|
52.9
|
1.0
|
CD1
|
D:ILE51
|
3.9
|
51.9
|
1.0
|
C12
|
D:EA7404
|
4.1
|
29.7
|
1.0
|
CB
|
D:VAL196
|
4.1
|
27.6
|
1.0
|
CD
|
D:LYS71
|
4.2
|
51.0
|
1.0
|
N
|
D:ASP197
|
4.3
|
29.6
|
1.0
|
CB
|
D:ASP197
|
4.3
|
32.8
|
1.0
|
C17
|
D:EA7404
|
4.5
|
32.9
|
1.0
|
CA
|
D:ASP197
|
4.6
|
30.6
|
1.0
|
N3
|
D:EA7404
|
4.6
|
31.2
|
1.0
|
F1
|
D:EA7404
|
4.7
|
32.0
|
1.0
|
N5
|
D:EA7404
|
4.8
|
30.9
|
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 Propynyl-Pteridinone Inhibitor To Be Published.
Page generated: Thu Aug 1 18:31:47 2024
|