Fluorine in PDB 6v2u: Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
Enzymatic activity of Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
All present enzymatic activity of Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib, PDB code: 6v2u
was solved by
K.Li,
G.Gonzalez Del-Pino,
E.Park,
M.J.Eck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.48 /
3.78
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.618,
89.618,
164.583,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
28.1 /
30.9
|
Other elements in 6v2u:
The structure of Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
(pdb code 6v2u). 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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib, PDB code: 6v2u:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:82.3
occ:1.00
|
F39
|
A:P06801
|
0.0
|
82.3
|
1.0
|
C32
|
A:P06801
|
1.4
|
78.0
|
1.0
|
C30
|
A:P06801
|
2.4
|
77.8
|
1.0
|
C31
|
A:P06801
|
2.4
|
77.7
|
1.0
|
C16
|
A:P06801
|
2.7
|
81.9
|
1.0
|
N40
|
A:P06801
|
2.7
|
82.9
|
1.0
|
N
|
A:ASP594
|
2.8
|
82.5
|
1.0
|
N15
|
A:P06801
|
3.0
|
85.1
|
1.0
|
CA
|
A:ASP594
|
3.2
|
90.4
|
1.0
|
CB
|
A:ASP594
|
3.2
|
97.9
|
1.0
|
C35
|
A:P06801
|
3.6
|
83.4
|
1.0
|
C33
|
A:P06801
|
3.6
|
78.4
|
1.0
|
C12
|
A:P06801
|
3.8
|
84.6
|
1.0
|
NZ
|
A:LYS483
|
3.8
|
91.0
|
1.0
|
C
|
A:GLY593
|
3.8
|
73.0
|
1.0
|
OD1
|
A:ASP594
|
4.0
|
0.8
|
1.0
|
CZ
|
A:PHE583
|
4.0
|
75.9
|
1.0
|
CE2
|
A:PHE583
|
4.1
|
74.6
|
1.0
|
C14
|
A:P06801
|
4.1
|
86.6
|
1.0
|
CG
|
A:ASP594
|
4.1
|
0.7
|
1.0
|
C37
|
A:P06801
|
4.1
|
83.5
|
1.0
|
CA
|
A:GLY593
|
4.3
|
69.5
|
1.0
|
S42
|
A:P06801
|
4.4
|
78.5
|
1.0
|
CD2
|
A:LEU514
|
4.5
|
79.7
|
1.0
|
S13
|
A:P06801
|
4.5
|
85.5
|
1.0
|
CE
|
A:LYS483
|
4.6
|
89.8
|
1.0
|
C4
|
A:P06801
|
4.6
|
72.1
|
1.0
|
C
|
A:ASP594
|
4.7
|
89.5
|
1.0
|
C2
|
A:P06801
|
4.7
|
81.5
|
1.0
|
O
|
A:GLY593
|
4.7
|
73.8
|
1.0
|
O55
|
A:P06801
|
4.9
|
76.0
|
1.0
|
O54
|
A:P06801
|
5.0
|
89.3
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:82.6
occ:1.00
|
F52
|
A:P06801
|
0.0
|
82.6
|
1.0
|
C49
|
A:P06801
|
1.4
|
80.2
|
1.0
|
C43
|
A:P06801
|
2.4
|
78.7
|
1.0
|
C50
|
A:P06801
|
2.4
|
82.6
|
1.0
|
O54
|
A:P06801
|
2.6
|
89.3
|
1.0
|
S42
|
A:P06801
|
3.0
|
78.5
|
1.0
|
CD1
|
A:LEU505
|
3.3
|
85.0
|
1.0
|
CG2
|
A:ILE527
|
3.3
|
77.1
|
1.0
|
CG2
|
A:THR529
|
3.4
|
75.0
|
1.0
|
C33
|
A:P06801
|
3.5
|
78.4
|
1.0
|
C47
|
A:P06801
|
3.6
|
82.1
|
1.0
|
C46
|
A:P06801
|
3.6
|
84.1
|
1.0
|
N40
|
A:P06801
|
4.1
|
82.9
|
1.0
|
O55
|
A:P06801
|
4.1
|
76.0
|
1.0
|
CB
|
A:ILE527
|
4.1
|
76.8
|
1.0
|
C44
|
A:P06801
|
4.1
|
85.8
|
1.0
|
CD1
|
A:ILE527
|
4.2
|
94.5
|
1.0
|
C31
|
A:P06801
|
4.3
|
77.7
|
1.0
|
CG
|
A:LEU505
|
4.4
|
85.3
|
1.0
|
CD2
|
A:LEU505
|
4.5
|
89.6
|
1.0
|
C37
|
A:P06801
|
4.5
|
83.5
|
1.0
|
CD
|
A:LYS483
|
4.5
|
95.4
|
1.0
|
NZ
|
A:LYS483
|
4.7
|
91.0
|
1.0
|
F53
|
A:P06801
|
4.8
|
84.7
|
1.0
|
CG1
|
A:ILE527
|
4.8
|
80.3
|
1.0
|
CB
|
A:THR529
|
4.9
|
71.7
|
1.0
|
CD1
|
A:PHE516
|
4.9
|
76.4
|
1.0
|
CB
|
A:LEU505
|
4.9
|
82.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:84.7
occ:1.00
|
F53
|
A:P06801
|
0.0
|
84.7
|
1.0
|
C46
|
A:P06801
|
1.4
|
84.1
|
1.0
|
C44
|
A:P06801
|
2.4
|
85.8
|
1.0
|
C43
|
A:P06801
|
2.4
|
78.7
|
1.0
|
S42
|
A:P06801
|
3.0
|
78.5
|
1.0
|
O55
|
A:P06801
|
3.1
|
76.0
|
1.0
|
CA
|
A:GLY593
|
3.3
|
69.5
|
1.0
|
N40
|
A:P06801
|
3.3
|
82.9
|
1.0
|
CE1
|
A:PHE595
|
3.5
|
69.3
|
1.0
|
C47
|
A:P06801
|
3.6
|
82.1
|
1.0
|
C49
|
A:P06801
|
3.6
|
80.2
|
1.0
|
CZ
|
A:PHE595
|
3.6
|
56.5
|
1.0
|
CD1
|
A:PHE595
|
3.7
|
73.7
|
1.0
|
N
|
A:ASP594
|
3.8
|
82.5
|
1.0
|
C
|
A:GLY593
|
3.9
|
73.0
|
1.0
|
CE2
|
A:PHE595
|
3.9
|
61.2
|
1.0
|
CG
|
A:PHE595
|
3.9
|
74.8
|
1.0
|
O
|
A:ILE592
|
4.0
|
73.6
|
1.0
|
CD2
|
A:PHE595
|
4.0
|
76.3
|
1.0
|
C50
|
A:P06801
|
4.1
|
82.6
|
1.0
|
CB
|
A:LEU514
|
4.3
|
73.7
|
1.0
|
O54
|
A:P06801
|
4.4
|
89.3
|
1.0
|
N
|
A:GLY593
|
4.4
|
72.3
|
1.0
|
CD2
|
A:LEU514
|
4.5
|
79.7
|
1.0
|
N
|
A:PHE595
|
4.5
|
86.4
|
1.0
|
C31
|
A:P06801
|
4.5
|
77.7
|
1.0
|
CD2
|
A:LEU505
|
4.6
|
89.6
|
1.0
|
C
|
A:ILE592
|
4.7
|
73.7
|
1.0
|
F52
|
A:P06801
|
4.8
|
82.6
|
1.0
|
CB
|
A:PHE595
|
4.8
|
74.3
|
1.0
|
O
|
A:GLY593
|
4.8
|
73.8
|
1.0
|
CA
|
A:ASP594
|
4.9
|
90.4
|
1.0
|
CG
|
A:LEU514
|
5.0
|
73.9
|
1.0
|
O
|
A:LEU514
|
5.0
|
78.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:65.3
occ:1.00
|
F39
|
B:P06801
|
0.0
|
65.3
|
1.0
|
C32
|
B:P06801
|
1.4
|
60.5
|
1.0
|
C30
|
B:P06801
|
2.4
|
59.1
|
1.0
|
C31
|
B:P06801
|
2.4
|
59.6
|
1.0
|
C16
|
B:P06801
|
2.7
|
60.7
|
1.0
|
N40
|
B:P06801
|
2.7
|
58.6
|
1.0
|
N
|
B:ASP594
|
2.9
|
67.6
|
1.0
|
N15
|
B:P06801
|
3.0
|
59.8
|
1.0
|
CA
|
B:ASP594
|
3.3
|
77.4
|
1.0
|
CB
|
B:ASP594
|
3.5
|
82.5
|
1.0
|
C35
|
B:P06801
|
3.6
|
58.9
|
1.0
|
C33
|
B:P06801
|
3.6
|
58.7
|
1.0
|
C12
|
B:P06801
|
3.8
|
60.8
|
1.0
|
C
|
B:GLY593
|
3.9
|
61.2
|
1.0
|
C14
|
B:P06801
|
4.1
|
55.2
|
1.0
|
C37
|
B:P06801
|
4.1
|
57.8
|
1.0
|
CZ
|
B:PHE583
|
4.1
|
62.6
|
1.0
|
CE2
|
B:PHE583
|
4.2
|
62.7
|
1.0
|
OD1
|
B:ASP594
|
4.2
|
85.5
|
1.0
|
NZ
|
B:LYS483
|
4.3
|
63.8
|
1.0
|
CA
|
B:GLY593
|
4.3
|
58.5
|
1.0
|
S42
|
B:P06801
|
4.3
|
55.5
|
1.0
|
CG
|
B:ASP594
|
4.4
|
86.1
|
1.0
|
S13
|
B:P06801
|
4.5
|
64.7
|
1.0
|
CD2
|
B:LEU514
|
4.6
|
66.0
|
1.0
|
C4
|
B:P06801
|
4.7
|
58.7
|
1.0
|
C2
|
B:P06801
|
4.7
|
57.8
|
1.0
|
C
|
B:ASP594
|
4.8
|
83.1
|
1.0
|
O
|
B:GLY593
|
4.9
|
57.0
|
1.0
|
O54
|
B:P06801
|
4.9
|
68.1
|
1.0
|
O55
|
B:P06801
|
4.9
|
62.5
|
1.0
|
CE
|
B:LYS483
|
5.0
|
67.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:60.1
occ:1.00
|
F52
|
B:P06801
|
0.0
|
60.1
|
1.0
|
C49
|
B:P06801
|
1.4
|
53.4
|
1.0
|
C43
|
B:P06801
|
2.4
|
55.6
|
1.0
|
C50
|
B:P06801
|
2.4
|
53.6
|
1.0
|
O54
|
B:P06801
|
2.6
|
68.1
|
1.0
|
S42
|
B:P06801
|
3.0
|
55.5
|
1.0
|
CD1
|
B:LEU505
|
3.3
|
59.5
|
1.0
|
CG2
|
B:ILE527
|
3.3
|
56.2
|
1.0
|
CG2
|
B:THR529
|
3.5
|
59.0
|
1.0
|
C33
|
B:P06801
|
3.5
|
58.7
|
1.0
|
C46
|
B:P06801
|
3.6
|
60.6
|
1.0
|
C47
|
B:P06801
|
3.6
|
58.7
|
1.0
|
O55
|
B:P06801
|
4.1
|
62.5
|
1.0
|
N40
|
B:P06801
|
4.1
|
58.6
|
1.0
|
C44
|
B:P06801
|
4.1
|
61.8
|
1.0
|
CB
|
B:ILE527
|
4.1
|
61.3
|
1.0
|
C31
|
B:P06801
|
4.3
|
59.6
|
1.0
|
CD1
|
B:ILE527
|
4.3
|
61.5
|
1.0
|
CG
|
B:LEU505
|
4.5
|
58.2
|
1.0
|
C37
|
B:P06801
|
4.5
|
57.8
|
1.0
|
CD2
|
B:LEU505
|
4.7
|
51.2
|
1.0
|
CD
|
B:LYS483
|
4.7
|
69.2
|
1.0
|
F53
|
B:P06801
|
4.8
|
61.7
|
1.0
|
CG1
|
B:ILE527
|
4.9
|
64.5
|
1.0
|
CB
|
B:THR529
|
5.0
|
55.8
|
1.0
|
CB
|
B:LEU505
|
5.0
|
62.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6v2u
Go back to
Fluorine Binding Sites List in 6v2u
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib
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 Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:61.7
occ:1.00
|
F53
|
B:P06801
|
0.0
|
61.7
|
1.0
|
C46
|
B:P06801
|
1.4
|
60.6
|
1.0
|
C44
|
B:P06801
|
2.4
|
61.8
|
1.0
|
C43
|
B:P06801
|
2.4
|
55.6
|
1.0
|
S42
|
B:P06801
|
3.0
|
55.5
|
1.0
|
O55
|
B:P06801
|
3.1
|
62.5
|
1.0
|
N40
|
B:P06801
|
3.3
|
58.6
|
1.0
|
CA
|
B:GLY593
|
3.3
|
58.5
|
1.0
|
CE1
|
B:PHE595
|
3.4
|
64.8
|
1.0
|
CZ
|
B:PHE595
|
3.5
|
51.1
|
1.0
|
CD1
|
B:PHE595
|
3.6
|
65.5
|
1.0
|
C47
|
B:P06801
|
3.6
|
58.7
|
1.0
|
C49
|
B:P06801
|
3.6
|
53.4
|
1.0
|
CE2
|
B:PHE595
|
3.8
|
48.7
|
1.0
|
CG
|
B:PHE595
|
3.9
|
59.6
|
1.0
|
C
|
B:GLY593
|
3.9
|
61.2
|
1.0
|
N
|
B:ASP594
|
3.9
|
67.6
|
1.0
|
CD2
|
B:PHE595
|
3.9
|
54.7
|
1.0
|
O
|
B:ILE592
|
4.0
|
53.1
|
1.0
|
C50
|
B:P06801
|
4.1
|
53.6
|
1.0
|
CB
|
B:LEU514
|
4.3
|
54.8
|
1.0
|
N
|
B:GLY593
|
4.4
|
60.0
|
1.0
|
O54
|
B:P06801
|
4.4
|
68.1
|
1.0
|
N
|
B:PHE595
|
4.5
|
77.6
|
1.0
|
C31
|
B:P06801
|
4.5
|
59.6
|
1.0
|
C
|
B:ILE592
|
4.6
|
54.0
|
1.0
|
CD2
|
B:LEU514
|
4.6
|
66.0
|
1.0
|
CB
|
B:PHE595
|
4.8
|
59.9
|
1.0
|
F52
|
B:P06801
|
4.8
|
60.1
|
1.0
|
O
|
B:GLY593
|
4.8
|
57.0
|
1.0
|
O
|
B:LEU514
|
4.9
|
64.3
|
1.0
|
CD2
|
B:LEU505
|
4.9
|
51.2
|
1.0
|
|
Reference:
K.Li,
G.Gonzalez Del-Pino,
E.Park,
M.J.Eck.
Crystal Structure of the Insect Cell-Expressed Wt-Braf Kinase in Complex with Dabrafenib To Be Published.
Page generated: Fri Aug 2 02:43:03 2024
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