Fluorine in PDB 7p3v: B-Raf V600E Structure Bound to A New Inhibitor
Enzymatic activity of B-Raf V600E Structure Bound to A New Inhibitor
All present enzymatic activity of B-Raf V600E Structure Bound to A New Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of B-Raf V600E Structure Bound to A New Inhibitor, PDB code: 7p3v
was solved by
M.Schneider,
M.Gelin,
M.Cohen-Gonsaud,
G.Labesse,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.55 /
2.37
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.632,
104.854,
109.557,
90,
90,
90
|
|
R / Rfree (%)
|
19.5 /
24.7
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the B-Raf V600E Structure Bound to A New Inhibitor
(pdb code 7p3v). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
B-Raf V600E Structure Bound to A New Inhibitor, PDB code: 7p3v:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 1 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:44.9
occ:1.00
|
F
|
A:5I4801
|
0.0
|
44.9
|
1.0
|
|
C11
|
A:5I4801
|
1.4
|
40.2
|
1.0
|
|
C10
|
A:5I4801
|
2.3
|
37.5
|
1.0
|
|
H10
|
A:5I4801
|
2.3
|
51.2
|
1.0
|
|
C6
|
A:5I4801
|
2.4
|
42.5
|
1.0
|
|
N1
|
A:5I4801
|
2.6
|
42.7
|
1.0
|
|
C5
|
A:5I4801
|
2.8
|
45.8
|
1.0
|
|
N
|
A:5I4801
|
2.8
|
50.2
|
1.0
|
|
N
|
A:ASP594
|
3.4
|
52.0
|
1.0
|
|
CB
|
A:ASP594
|
3.5
|
55.6
|
1.0
|
|
CE2
|
A:PHE583
|
3.6
|
49.2
|
1.0
|
|
O
|
A:HOH927
|
3.6
|
51.5
|
1.0
|
|
C7
|
A:5I4801
|
3.6
|
44.0
|
1.0
|
|
CA
|
A:ASP594
|
3.6
|
54.7
|
1.0
|
|
C9
|
A:5I4801
|
3.7
|
41.7
|
1.0
|
|
CZ
|
A:PHE583
|
3.7
|
49.6
|
1.0
|
|
OD2
|
A:ASP594
|
3.9
|
66.6
|
1.0
|
|
C4
|
A:5I4801
|
3.9
|
54.4
|
1.0
|
|
C18
|
A:5I4801
|
4.0
|
47.1
|
1.0
|
|
CG
|
A:ASP594
|
4.0
|
63.7
|
1.0
|
|
H14
|
A:5I4801
|
4.1
|
57.5
|
1.0
|
|
C
|
A:GLY593
|
4.1
|
51.7
|
1.0
|
|
C8
|
A:5I4801
|
4.1
|
41.9
|
1.0
|
|
CD2
|
A:LEU514
|
4.2
|
42.4
|
1.0
|
|
S
|
A:5I4801
|
4.3
|
48.3
|
1.0
|
|
CA
|
A:GLY593
|
4.3
|
52.0
|
1.0
|
|
H7
|
A:5I4801
|
4.4
|
52.8
|
1.0
|
|
H9
|
A:5I4801
|
4.4
|
50.0
|
1.0
|
|
H
|
A:5I4801
|
4.6
|
64.4
|
1.0
|
|
NZ
|
A:LYS483
|
4.7
|
56.4
|
1.0
|
|
CE
|
A:LYS483
|
4.7
|
50.0
|
1.0
|
|
C20
|
A:5I4801
|
4.7
|
48.0
|
1.0
|
|
C19
|
A:5I4801
|
4.8
|
51.0
|
1.0
|
|
CD2
|
A:PHE583
|
4.8
|
49.8
|
1.0
|
|
S1
|
A:5I4801
|
4.9
|
47.0
|
1.0
|
|
O2
|
A:5I4801
|
4.9
|
46.3
|
1.0
|
|
C3
|
A:5I4801
|
4.9
|
53.7
|
1.0
|
|
F2
|
A:5I4801
|
5.0
|
50.1
|
1.0
|
|
O
|
A:GLY593
|
5.0
|
50.7
|
1.0
|
|
OD1
|
A:ASP594
|
5.0
|
67.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 2 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:48.1
occ:1.00
|
F1
|
A:5I4801
|
0.0
|
48.1
|
1.0
|
|
C16
|
A:5I4801
|
1.4
|
47.9
|
1.0
|
|
C17
|
A:5I4801
|
2.3
|
48.7
|
1.0
|
|
H13
|
A:5I4801
|
2.4
|
58.5
|
1.0
|
|
C15
|
A:5I4801
|
2.5
|
45.1
|
1.0
|
|
H12
|
A:5I4801
|
2.7
|
54.1
|
1.0
|
|
CD1
|
A:PHE516
|
3.1
|
46.9
|
1.0
|
|
CG2
|
A:THR529
|
3.1
|
42.3
|
1.0
|
|
CG2
|
A:ILE527
|
3.2
|
49.9
|
1.0
|
|
CB
|
A:PHE516
|
3.3
|
46.4
|
1.0
|
|
CD1
|
A:LEU505
|
3.3
|
55.9
|
1.0
|
|
CA
|
A:PHE516
|
3.3
|
43.5
|
1.0
|
|
CG
|
A:PHE516
|
3.6
|
50.7
|
1.0
|
|
C12
|
A:5I4801
|
3.7
|
47.8
|
1.0
|
|
C14
|
A:5I4801
|
3.7
|
46.3
|
1.0
|
|
N
|
A:PHE516
|
4.0
|
40.7
|
1.0
|
|
CB
|
A:LEU505
|
4.1
|
54.7
|
1.0
|
|
CG
|
A:LEU505
|
4.2
|
55.9
|
1.0
|
|
O
|
A:VAL528
|
4.2
|
43.0
|
1.0
|
|
CE1
|
A:PHE516
|
4.2
|
45.0
|
1.0
|
|
C13
|
A:5I4801
|
4.2
|
49.0
|
1.0
|
|
CB
|
A:THR529
|
4.4
|
43.6
|
1.0
|
|
H9
|
A:5I4801
|
4.5
|
50.0
|
1.0
|
|
H11
|
A:5I4801
|
4.5
|
55.5
|
1.0
|
|
CD2
|
A:LEU505
|
4.5
|
52.9
|
1.0
|
|
C
|
A:PHE516
|
4.6
|
45.7
|
1.0
|
|
CB
|
A:ILE527
|
4.7
|
51.2
|
1.0
|
|
C
|
A:LEU515
|
4.7
|
44.6
|
1.0
|
|
O
|
A:LEU515
|
4.7
|
44.6
|
1.0
|
|
N
|
A:MET517
|
4.8
|
44.8
|
1.0
|
|
C
|
A:VAL528
|
4.9
|
43.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 3 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:50.1
occ:1.00
|
F2
|
A:5I4801
|
0.0
|
50.1
|
1.0
|
|
C13
|
A:5I4801
|
1.4
|
49.0
|
1.0
|
|
C12
|
A:5I4801
|
2.3
|
47.8
|
1.0
|
|
C14
|
A:5I4801
|
2.5
|
46.3
|
1.0
|
|
H11
|
A:5I4801
|
2.7
|
55.5
|
1.0
|
|
S
|
A:5I4801
|
2.9
|
48.3
|
1.0
|
|
H10
|
A:5I4801
|
2.9
|
51.2
|
1.0
|
|
CA
|
A:GLY593
|
3.0
|
52.0
|
1.0
|
|
N
|
A:ASP594
|
3.1
|
52.0
|
1.0
|
|
N1
|
A:5I4801
|
3.1
|
42.7
|
1.0
|
|
O1
|
A:5I4801
|
3.2
|
50.8
|
1.0
|
|
C
|
A:GLY593
|
3.4
|
51.7
|
1.0
|
|
CE1
|
A:PHE595
|
3.5
|
65.6
|
1.0
|
|
C15
|
A:5I4801
|
3.7
|
45.1
|
1.0
|
|
C17
|
A:5I4801
|
3.7
|
48.7
|
1.0
|
|
CD1
|
A:PHE595
|
3.8
|
66.7
|
1.0
|
|
CD2
|
A:LEU514
|
3.9
|
42.4
|
1.0
|
|
O
|
A:ILE592
|
3.9
|
50.3
|
1.0
|
|
CZ
|
A:PHE595
|
4.0
|
64.1
|
1.0
|
|
CB
|
A:LEU514
|
4.0
|
45.1
|
1.0
|
|
C10
|
A:5I4801
|
4.2
|
37.5
|
1.0
|
|
N
|
A:GLY593
|
4.2
|
51.8
|
1.0
|
|
C16
|
A:5I4801
|
4.2
|
47.9
|
1.0
|
|
CA
|
A:ASP594
|
4.2
|
54.7
|
1.0
|
|
N
|
A:PHE595
|
4.3
|
56.8
|
1.0
|
|
O2
|
A:5I4801
|
4.3
|
46.3
|
1.0
|
|
H13
|
A:5I4801
|
4.4
|
58.5
|
1.0
|
|
O
|
A:GLY593
|
4.4
|
50.7
|
1.0
|
|
CG
|
A:PHE595
|
4.5
|
65.2
|
1.0
|
|
H12
|
A:5I4801
|
4.5
|
54.1
|
1.0
|
|
C
|
A:ILE592
|
4.5
|
51.0
|
1.0
|
|
CG
|
A:LEU514
|
4.5
|
42.0
|
1.0
|
|
CE2
|
A:PHE595
|
4.6
|
62.0
|
1.0
|
|
H9
|
A:5I4801
|
4.7
|
50.0
|
1.0
|
|
C
|
A:ASP594
|
4.8
|
55.8
|
1.0
|
|
CD2
|
A:PHE595
|
4.8
|
64.3
|
1.0
|
|
C9
|
A:5I4801
|
4.9
|
41.7
|
1.0
|
|
O
|
A:LEU514
|
4.9
|
48.0
|
1.0
|
|
C11
|
A:5I4801
|
5.0
|
40.2
|
1.0
|
|
F
|
A:5I4801
|
5.0
|
44.9
|
1.0
|
|
CD2
|
A:LEU505
|
5.0
|
52.9
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 4 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:55.2
occ:1.00
|
F
|
B:5I4801
|
0.0
|
55.2
|
1.0
|
|
C11
|
B:5I4801
|
1.3
|
54.0
|
1.0
|
|
C10
|
B:5I4801
|
2.3
|
52.3
|
1.0
|
|
H10
|
B:5I4801
|
2.4
|
68.0
|
1.0
|
|
C6
|
B:5I4801
|
2.4
|
56.7
|
1.0
|
|
N1
|
B:5I4801
|
2.6
|
56.6
|
1.0
|
|
N
|
B:5I4801
|
2.7
|
62.1
|
1.0
|
|
C5
|
B:5I4801
|
2.7
|
61.2
|
1.0
|
|
O
|
B:HOH912
|
3.1
|
58.7
|
1.0
|
|
N
|
B:ASP594
|
3.3
|
76.2
|
1.0
|
|
CB
|
B:ASP594
|
3.4
|
75.4
|
1.0
|
|
CG
|
B:ASP594
|
3.5
|
77.9
|
1.0
|
|
CA
|
B:ASP594
|
3.5
|
75.6
|
1.0
|
|
CZ
|
B:PHE583
|
3.6
|
61.0
|
1.0
|
|
C7
|
B:5I4801
|
3.6
|
57.2
|
1.0
|
|
C9
|
B:5I4801
|
3.7
|
53.6
|
1.0
|
|
CE2
|
B:PHE583
|
3.7
|
59.2
|
1.0
|
|
OD2
|
B:ASP594
|
3.8
|
79.4
|
1.0
|
|
OD1
|
B:ASP594
|
3.8
|
79.0
|
1.0
|
|
C4
|
B:5I4801
|
3.8
|
65.1
|
1.0
|
|
C18
|
B:5I4801
|
3.9
|
65.7
|
1.0
|
|
H14
|
B:5I4801
|
4.1
|
69.0
|
1.0
|
|
C8
|
B:5I4801
|
4.2
|
55.5
|
1.0
|
|
C
|
B:GLY593
|
4.2
|
73.9
|
1.0
|
|
S
|
B:5I4801
|
4.3
|
54.8
|
1.0
|
|
H7
|
B:5I4801
|
4.4
|
68.7
|
1.0
|
|
NZ
|
B:LYS483
|
4.4
|
61.2
|
1.0
|
|
H18
|
B:5I4801
|
4.4
|
90.8
|
1.0
|
|
H9
|
B:5I4801
|
4.4
|
64.4
|
1.0
|
|
CD2
|
B:LEU514
|
4.6
|
53.7
|
1.0
|
|
CA
|
B:GLY593
|
4.6
|
75.0
|
1.0
|
|
H
|
B:5I4801
|
4.6
|
82.2
|
1.0
|
|
C20
|
B:5I4801
|
4.7
|
57.5
|
1.0
|
|
C19
|
B:5I4801
|
4.8
|
60.2
|
1.0
|
|
C3
|
B:5I4801
|
4.8
|
68.5
|
0.8
|
|
S1
|
B:5I4801
|
4.8
|
65.0
|
1.0
|
|
CE1
|
B:PHE583
|
4.8
|
61.7
|
1.0
|
|
O2
|
B:5I4801
|
4.9
|
50.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 5 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:53.0
occ:1.00
|
F1
|
B:5I4801
|
0.0
|
53.0
|
1.0
|
|
C16
|
B:5I4801
|
1.4
|
54.7
|
1.0
|
|
C17
|
B:5I4801
|
2.3
|
56.3
|
1.0
|
|
H13
|
B:5I4801
|
2.4
|
67.6
|
1.0
|
|
C15
|
B:5I4801
|
2.5
|
51.2
|
1.0
|
|
H12
|
B:5I4801
|
2.7
|
61.5
|
1.0
|
|
CG2
|
B:THR529
|
3.0
|
51.2
|
1.0
|
|
CB
|
B:PHE516
|
3.1
|
49.3
|
1.0
|
|
CA
|
B:PHE516
|
3.2
|
47.8
|
1.0
|
|
CD1
|
B:PHE516
|
3.3
|
54.5
|
1.0
|
|
CG2
|
B:ILE527
|
3.3
|
58.8
|
1.0
|
|
CG
|
B:PHE516
|
3.7
|
52.8
|
1.0
|
|
C14
|
B:5I4801
|
3.7
|
54.5
|
1.0
|
|
C12
|
B:5I4801
|
3.7
|
56.6
|
1.0
|
|
N
|
B:PHE516
|
3.8
|
51.2
|
1.0
|
|
CD1
|
B:LEU505
|
3.8
|
54.8
|
1.0
|
|
O
|
B:VAL528
|
4.1
|
55.2
|
1.0
|
|
C13
|
B:5I4801
|
4.2
|
56.8
|
1.0
|
|
CB
|
B:LEU505
|
4.2
|
55.0
|
1.0
|
|
CB
|
B:THR529
|
4.2
|
51.1
|
1.0
|
|
CD2
|
B:LEU505
|
4.3
|
55.7
|
1.0
|
|
CG
|
B:LEU505
|
4.3
|
58.2
|
1.0
|
|
H11
|
B:5I4801
|
4.4
|
65.4
|
1.0
|
|
C
|
B:PHE516
|
4.4
|
52.1
|
1.0
|
|
C
|
B:LEU515
|
4.5
|
51.6
|
1.0
|
|
O
|
B:LEU515
|
4.5
|
49.2
|
1.0
|
|
H9
|
B:5I4801
|
4.5
|
64.4
|
1.0
|
|
CE1
|
B:PHE516
|
4.5
|
58.5
|
1.0
|
|
N
|
B:MET517
|
4.7
|
53.4
|
1.0
|
|
C
|
B:VAL528
|
4.7
|
55.0
|
1.0
|
|
CA
|
B:THR529
|
4.7
|
51.7
|
1.0
|
|
CB
|
B:ILE527
|
4.9
|
58.7
|
1.0
|
|
O2
|
B:5I4801
|
5.0
|
50.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7p3v
Go back to
Fluorine Binding Sites List in 7p3v
Fluorine binding site 6 out
of 6 in the B-Raf V600E Structure Bound to A New Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of B-Raf V600E Structure Bound to A New Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:58.1
occ:1.00
|
F2
|
B:5I4801
|
0.0
|
58.1
|
1.0
|
|
C13
|
B:5I4801
|
1.4
|
56.8
|
1.0
|
|
C12
|
B:5I4801
|
2.4
|
56.6
|
1.0
|
|
C14
|
B:5I4801
|
2.5
|
54.5
|
1.0
|
|
H11
|
B:5I4801
|
2.7
|
65.4
|
1.0
|
|
CA
|
B:GLY593
|
3.1
|
75.0
|
1.0
|
|
S
|
B:5I4801
|
3.1
|
54.8
|
1.0
|
|
CE2
|
B:PHE595
|
3.1
|
78.6
|
1.0
|
|
CD2
|
B:PHE595
|
3.1
|
77.8
|
1.0
|
|
O1
|
B:5I4801
|
3.3
|
58.9
|
1.0
|
|
N
|
B:ASP594
|
3.4
|
76.2
|
1.0
|
|
H10
|
B:5I4801
|
3.5
|
68.0
|
1.0
|
|
N1
|
B:5I4801
|
3.5
|
56.6
|
1.0
|
|
C
|
B:GLY593
|
3.6
|
73.9
|
1.0
|
|
C15
|
B:5I4801
|
3.7
|
51.2
|
1.0
|
|
C17
|
B:5I4801
|
3.7
|
56.3
|
1.0
|
|
O
|
B:ILE592
|
3.9
|
60.0
|
1.0
|
|
CB
|
B:LEU514
|
4.0
|
52.0
|
1.0
|
|
CD2
|
B:LEU514
|
4.1
|
53.7
|
1.0
|
|
C16
|
B:5I4801
|
4.2
|
54.7
|
1.0
|
|
N
|
B:GLY593
|
4.3
|
72.7
|
1.0
|
|
CZ
|
B:PHE595
|
4.3
|
76.8
|
1.0
|
|
CG
|
B:PHE595
|
4.3
|
75.0
|
1.0
|
|
N
|
B:PHE595
|
4.3
|
73.7
|
1.0
|
|
H12
|
B:5I4801
|
4.4
|
61.5
|
1.0
|
|
H13
|
B:5I4801
|
4.5
|
67.6
|
1.0
|
|
C10
|
B:5I4801
|
4.5
|
52.3
|
1.0
|
|
CA
|
B:ASP594
|
4.5
|
75.6
|
1.0
|
|
C
|
B:ILE592
|
4.5
|
58.7
|
1.0
|
|
O2
|
B:5I4801
|
4.5
|
50.5
|
1.0
|
|
O
|
B:GLY593
|
4.6
|
71.3
|
1.0
|
|
CG
|
B:LEU514
|
4.7
|
50.2
|
1.0
|
|
CD2
|
B:LEU505
|
4.7
|
55.7
|
1.0
|
|
C
|
B:ASP594
|
4.9
|
72.9
|
1.0
|
|
O
|
B:LEU514
|
4.9
|
47.7
|
1.0
|
|
H9
|
B:5I4801
|
4.9
|
64.4
|
1.0
|
|
Reference:
M.Schneider,
M.Gelin,
V.Delfosse,
M.Grimaldi,
M.Granell,
L.Heriaud,
J.-L.Pons,
M.Cohen-Gonsaud,
P.Balaguer,
W.Bourguet,
G.Labesse.
Structure-Based and Knowledge-Informed Design of B-Raf Inhibitors Devoid of Deleterious Pxr Binding To Be Published.
Page generated: Fri Nov 5 13:17:19 2021
|
