Fluorine in PDB 7k0v: Crystal Structure of Braf in Complex with Inhibitor Gne-0749
Enzymatic activity of Crystal Structure of Braf in Complex with Inhibitor Gne-0749
All present enzymatic activity of Crystal Structure of Braf in Complex with Inhibitor Gne-0749:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of Braf in Complex with Inhibitor Gne-0749, PDB code: 7k0v
was solved by
J.Yin,
C.E.Eigenbrot,
W.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.27 /
1.93
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.254,
115.354,
119.39,
90,
90,
90
|
R / Rfree (%)
|
18.4 /
23
|
Other elements in 7k0v:
The structure of Crystal Structure of Braf in Complex with Inhibitor Gne-0749 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
(pdb code 7k0v). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of Braf in Complex with Inhibitor Gne-0749, PDB code: 7k0v:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 1 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:27.9
occ:1.00
|
F15
|
A:VQP801
|
0.0
|
27.9
|
1.0
|
C14
|
A:VQP801
|
1.4
|
25.9
|
1.0
|
C9
|
A:VQP801
|
2.4
|
24.3
|
1.0
|
C13
|
A:VQP801
|
2.4
|
23.4
|
1.0
|
O17
|
A:VQP801
|
2.5
|
28.1
|
1.0
|
N8
|
A:VQP801
|
2.6
|
22.8
|
1.0
|
C16
|
A:VQP801
|
2.8
|
25.5
|
1.0
|
C10
|
A:VQP801
|
3.6
|
22.9
|
1.0
|
C12
|
A:VQP801
|
3.7
|
23.2
|
1.0
|
CD1
|
A:LEU597
|
3.7
|
35.6
|
1.0
|
CD1
|
A:PHE595
|
3.7
|
27.5
|
1.0
|
CG1
|
A:VAL471
|
3.8
|
23.8
|
1.0
|
CG2
|
A:VAL471
|
4.0
|
28.1
|
1.0
|
C7
|
A:VQP801
|
4.0
|
23.9
|
1.0
|
C11
|
A:VQP801
|
4.1
|
21.2
|
1.0
|
N18
|
A:VQP801
|
4.2
|
23.3
|
1.0
|
CA
|
A:PHE595
|
4.2
|
30.0
|
1.0
|
CB
|
A:VAL471
|
4.3
|
29.1
|
1.0
|
CG
|
A:LEU597
|
4.4
|
37.7
|
1.0
|
O
|
A:ASP594
|
4.4
|
31.4
|
1.0
|
CE1
|
A:PHE595
|
4.5
|
24.9
|
1.0
|
CB
|
A:PHE595
|
4.5
|
28.2
|
1.0
|
CG
|
A:PHE595
|
4.6
|
28.8
|
1.0
|
CD2
|
A:LEU597
|
4.7
|
37.8
|
1.0
|
N20
|
A:VQP801
|
4.7
|
26.4
|
1.0
|
O
|
A:PHE595
|
4.7
|
31.1
|
1.0
|
C
|
A:PHE595
|
4.8
|
32.0
|
1.0
|
C6
|
A:VQP801
|
4.8
|
26.1
|
1.0
|
C1
|
A:VQP801
|
4.8
|
26.1
|
1.0
|
C2
|
A:VQP801
|
4.8
|
23.8
|
1.0
|
C19
|
A:VQP801
|
4.9
|
25.9
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 2 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:26.6
occ:1.00
|
F32
|
A:VQP801
|
0.0
|
26.6
|
1.0
|
C4
|
A:VQP801
|
1.3
|
24.7
|
1.0
|
C3
|
A:VQP801
|
2.3
|
24.7
|
1.0
|
C5
|
A:VQP801
|
2.3
|
25.2
|
1.0
|
N22
|
A:VQP801
|
2.7
|
25.0
|
1.0
|
CD1
|
A:LEU505
|
3.2
|
25.9
|
1.0
|
CG2
|
A:ILE527
|
3.2
|
23.6
|
1.0
|
OE1
|
A:GLU501
|
3.5
|
32.1
|
1.0
|
C2
|
A:VQP801
|
3.6
|
23.8
|
1.0
|
C6
|
A:VQP801
|
3.6
|
26.1
|
1.0
|
CD1
|
A:ILE527
|
3.7
|
27.5
|
1.0
|
CB
|
A:ILE527
|
3.8
|
23.9
|
1.0
|
CD
|
A:GLU501
|
3.8
|
31.5
|
1.0
|
C23
|
A:VQP801
|
3.8
|
23.2
|
1.0
|
CE
|
A:LYS483
|
4.0
|
37.1
|
1.0
|
C7
|
A:VQP801
|
4.1
|
23.9
|
1.0
|
CG
|
A:GLU501
|
4.2
|
28.9
|
1.0
|
NZ
|
A:LYS483
|
4.2
|
39.9
|
1.0
|
CG1
|
A:ILE527
|
4.3
|
26.4
|
1.0
|
CG2
|
A:THR529
|
4.4
|
20.3
|
1.0
|
OE2
|
A:GLU501
|
4.4
|
36.8
|
1.0
|
O24
|
A:VQP801
|
4.5
|
23.1
|
1.0
|
N25
|
A:VQP801
|
4.6
|
26.7
|
1.0
|
CG
|
A:LEU505
|
4.6
|
27.6
|
1.0
|
C1
|
A:VQP801
|
4.8
|
26.1
|
1.0
|
CD
|
A:LYS483
|
4.9
|
33.0
|
1.0
|
CB
|
A:LYS483
|
4.9
|
27.9
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 3 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:29.4
occ:1.00
|
F15
|
B:VQP801
|
0.0
|
29.4
|
1.0
|
C14
|
B:VQP801
|
1.4
|
28.9
|
1.0
|
C9
|
B:VQP801
|
2.3
|
28.5
|
1.0
|
C13
|
B:VQP801
|
2.4
|
27.7
|
1.0
|
N8
|
B:VQP801
|
2.6
|
27.3
|
1.0
|
O17
|
B:VQP801
|
2.7
|
33.4
|
1.0
|
C16
|
B:VQP801
|
2.9
|
28.7
|
1.0
|
CG1
|
B:VAL471
|
3.6
|
31.6
|
1.0
|
C10
|
B:VQP801
|
3.6
|
25.9
|
1.0
|
CD1
|
B:PHE595
|
3.6
|
30.9
|
1.0
|
CG2
|
B:VAL471
|
3.7
|
34.6
|
1.0
|
C12
|
B:VQP801
|
3.7
|
27.5
|
1.0
|
CD2
|
B:LEU597
|
3.9
|
61.8
|
1.0
|
C7
|
B:VQP801
|
3.9
|
28.7
|
1.0
|
O
|
B:ASP594
|
4.0
|
38.7
|
1.0
|
CA
|
B:PHE595
|
4.0
|
36.9
|
1.0
|
CB
|
B:VAL471
|
4.1
|
33.7
|
1.0
|
C11
|
B:VQP801
|
4.1
|
27.2
|
1.0
|
N18
|
B:VQP801
|
4.3
|
29.2
|
1.0
|
CE1
|
B:PHE595
|
4.3
|
30.8
|
1.0
|
O
|
B:PHE595
|
4.4
|
44.1
|
1.0
|
CG
|
B:PHE595
|
4.4
|
31.8
|
1.0
|
CB
|
B:PHE595
|
4.5
|
32.4
|
1.0
|
C
|
B:PHE595
|
4.6
|
41.5
|
1.0
|
CG
|
B:LEU597
|
4.6
|
72.6
|
1.0
|
C1
|
B:VQP801
|
4.6
|
26.8
|
1.0
|
C2
|
B:VQP801
|
4.7
|
27.7
|
1.0
|
N20
|
B:VQP801
|
4.8
|
28.6
|
1.0
|
C6
|
B:VQP801
|
4.8
|
29.4
|
1.0
|
C
|
B:ASP594
|
4.9
|
34.2
|
1.0
|
N
|
B:PHE595
|
5.0
|
34.4
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 4 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:31.3
occ:1.00
|
F32
|
B:VQP801
|
0.0
|
31.3
|
1.0
|
C4
|
B:VQP801
|
1.3
|
29.0
|
1.0
|
C3
|
B:VQP801
|
2.3
|
27.5
|
1.0
|
C5
|
B:VQP801
|
2.3
|
27.6
|
1.0
|
N22
|
B:VQP801
|
2.7
|
25.7
|
1.0
|
CD1
|
B:LEU505
|
3.1
|
28.2
|
1.0
|
CG2
|
B:ILE527
|
3.2
|
28.3
|
1.0
|
OE2
|
B:GLU501
|
3.5
|
33.0
|
1.0
|
C2
|
B:VQP801
|
3.6
|
27.7
|
1.0
|
C6
|
B:VQP801
|
3.6
|
29.4
|
1.0
|
CB
|
B:ILE527
|
3.7
|
29.7
|
1.0
|
CE
|
B:LYS483
|
3.8
|
34.5
|
1.0
|
CD1
|
B:ILE527
|
3.9
|
33.2
|
1.0
|
CD
|
B:GLU501
|
3.9
|
33.3
|
1.0
|
C23
|
B:VQP801
|
3.9
|
26.2
|
1.0
|
C7
|
B:VQP801
|
4.1
|
28.7
|
1.0
|
CG2
|
B:THR529
|
4.2
|
23.2
|
1.0
|
CG1
|
B:ILE527
|
4.4
|
31.7
|
1.0
|
CG
|
B:GLU501
|
4.4
|
34.2
|
1.0
|
OE1
|
B:GLU501
|
4.4
|
29.7
|
1.0
|
CG
|
B:LEU505
|
4.4
|
27.9
|
1.0
|
O24
|
B:VQP801
|
4.6
|
26.5
|
1.0
|
N25
|
B:VQP801
|
4.6
|
27.9
|
1.0
|
CD2
|
B:LEU505
|
4.7
|
24.9
|
1.0
|
CB
|
B:LYS483
|
4.7
|
32.4
|
1.0
|
CD
|
B:LYS483
|
4.7
|
37.5
|
1.0
|
C1
|
B:VQP801
|
4.8
|
26.8
|
1.0
|
NZ
|
B:LYS483
|
4.9
|
37.1
|
1.0
|
CA
|
B:ILE527
|
5.0
|
31.8
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 5 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F801
b:27.4
occ:1.00
|
F15
|
C:VQP801
|
0.0
|
27.4
|
1.0
|
C14
|
C:VQP801
|
1.4
|
24.8
|
1.0
|
C9
|
C:VQP801
|
2.3
|
24.6
|
1.0
|
C13
|
C:VQP801
|
2.4
|
27.9
|
1.0
|
O17
|
C:VQP801
|
2.6
|
25.7
|
1.0
|
N8
|
C:VQP801
|
2.6
|
24.2
|
1.0
|
C16
|
C:VQP801
|
2.9
|
27.8
|
1.0
|
O
|
C:HOH977
|
3.3
|
30.2
|
1.0
|
CD1
|
C:PHE595
|
3.4
|
27.2
|
1.0
|
CG1
|
C:VAL471
|
3.6
|
25.9
|
1.0
|
C10
|
C:VQP801
|
3.6
|
22.4
|
1.0
|
C12
|
C:VQP801
|
3.7
|
25.6
|
1.0
|
O
|
C:HOH971
|
3.8
|
36.5
|
1.0
|
C7
|
C:VQP801
|
4.0
|
24.0
|
1.0
|
CG2
|
C:VAL471
|
4.1
|
29.2
|
1.0
|
C11
|
C:VQP801
|
4.1
|
23.6
|
1.0
|
CE1
|
C:PHE595
|
4.2
|
24.1
|
1.0
|
CB
|
C:PHE595
|
4.2
|
26.6
|
1.0
|
CG
|
C:PHE595
|
4.2
|
25.9
|
1.0
|
N18
|
C:VQP801
|
4.2
|
29.9
|
1.0
|
CB
|
C:VAL471
|
4.3
|
29.5
|
1.0
|
CA
|
C:PHE595
|
4.7
|
27.3
|
1.0
|
C1
|
C:VQP801
|
4.7
|
24.4
|
1.0
|
N20
|
C:VQP801
|
4.8
|
27.2
|
1.0
|
C2
|
C:VQP801
|
4.8
|
24.6
|
1.0
|
C6
|
C:VQP801
|
4.9
|
23.1
|
1.0
|
C19
|
C:VQP801
|
5.0
|
26.9
|
1.0
|
O
|
C:PHE595
|
5.0
|
30.6
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 6 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
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 Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F801
b:25.7
occ:1.00
|
F32
|
C:VQP801
|
0.0
|
25.7
|
1.0
|
C4
|
C:VQP801
|
1.3
|
26.0
|
1.0
|
C3
|
C:VQP801
|
2.3
|
23.1
|
1.0
|
C5
|
C:VQP801
|
2.4
|
25.2
|
1.0
|
N22
|
C:VQP801
|
2.7
|
24.7
|
1.0
|
CD1
|
C:LEU505
|
3.2
|
21.7
|
1.0
|
CG2
|
C:ILE527
|
3.3
|
22.3
|
1.0
|
C2
|
C:VQP801
|
3.6
|
24.6
|
1.0
|
C6
|
C:VQP801
|
3.6
|
23.1
|
1.0
|
CB
|
C:ILE527
|
3.7
|
23.2
|
1.0
|
OE2
|
C:GLU501
|
3.7
|
29.1
|
1.0
|
C23
|
C:VQP801
|
3.8
|
25.2
|
1.0
|
CD
|
C:GLU501
|
3.8
|
27.0
|
1.0
|
CD1
|
C:ILE527
|
3.9
|
24.4
|
1.0
|
C7
|
C:VQP801
|
4.1
|
24.0
|
1.0
|
CG2
|
C:THR529
|
4.1
|
17.3
|
1.0
|
OE1
|
C:GLU501
|
4.2
|
28.9
|
1.0
|
CE
|
C:LYS483
|
4.3
|
27.8
|
1.0
|
CG
|
C:GLU501
|
4.3
|
25.0
|
1.0
|
NZ
|
C:LYS483
|
4.4
|
29.2
|
1.0
|
CG1
|
C:ILE527
|
4.5
|
22.4
|
1.0
|
N25
|
C:VQP801
|
4.5
|
25.4
|
1.0
|
O24
|
C:VQP801
|
4.5
|
22.6
|
1.0
|
CG
|
C:LEU505
|
4.6
|
23.3
|
1.0
|
CD
|
C:LYS483
|
4.7
|
28.5
|
1.0
|
C1
|
C:VQP801
|
4.8
|
24.4
|
1.0
|
CB
|
C:LYS483
|
4.9
|
28.4
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 7 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F801
b:28.5
occ:1.00
|
F15
|
D:VQP801
|
0.0
|
28.5
|
1.0
|
C14
|
D:VQP801
|
1.4
|
28.6
|
1.0
|
C9
|
D:VQP801
|
2.4
|
26.0
|
1.0
|
C13
|
D:VQP801
|
2.4
|
30.3
|
1.0
|
O17
|
D:VQP801
|
2.6
|
28.2
|
1.0
|
N8
|
D:VQP801
|
2.7
|
25.6
|
1.0
|
C16
|
D:VQP801
|
2.9
|
29.1
|
1.0
|
O
|
D:HOH956
|
3.3
|
30.6
|
1.0
|
CD1
|
D:PHE595
|
3.5
|
28.8
|
1.0
|
CG1
|
D:VAL471
|
3.6
|
27.3
|
1.0
|
C10
|
D:VQP801
|
3.6
|
26.8
|
1.0
|
C12
|
D:VQP801
|
3.7
|
28.4
|
1.0
|
CG2
|
D:VAL471
|
4.0
|
34.2
|
1.0
|
C7
|
D:VQP801
|
4.1
|
26.8
|
1.0
|
C11
|
D:VQP801
|
4.1
|
28.9
|
1.0
|
N18
|
D:VQP801
|
4.2
|
32.2
|
1.0
|
CB
|
D:PHE595
|
4.3
|
27.9
|
1.0
|
CB
|
D:VAL471
|
4.3
|
33.4
|
1.0
|
CE1
|
D:PHE595
|
4.3
|
28.9
|
1.0
|
CG
|
D:PHE595
|
4.3
|
28.2
|
1.0
|
CA
|
D:PHE595
|
4.8
|
30.1
|
1.0
|
N20
|
D:VQP801
|
4.8
|
28.8
|
1.0
|
C1
|
D:VQP801
|
4.8
|
25.1
|
1.0
|
O
|
D:PHE595
|
4.8
|
32.1
|
1.0
|
C6
|
D:VQP801
|
4.9
|
28.5
|
1.0
|
C2
|
D:VQP801
|
4.9
|
26.7
|
1.0
|
C19
|
D:VQP801
|
5.0
|
27.7
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 7k0v
Go back to
Fluorine Binding Sites List in 7k0v
Fluorine binding site 8 out
of 8 in the Crystal Structure of Braf in Complex with Inhibitor Gne-0749
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Braf in Complex with Inhibitor Gne-0749 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F801
b:28.6
occ:1.00
|
F32
|
D:VQP801
|
0.0
|
28.6
|
1.0
|
C4
|
D:VQP801
|
1.3
|
27.3
|
1.0
|
C5
|
D:VQP801
|
2.3
|
27.9
|
1.0
|
C3
|
D:VQP801
|
2.3
|
25.2
|
1.0
|
N22
|
D:VQP801
|
2.6
|
24.9
|
1.0
|
CD1
|
D:LEU505
|
3.2
|
28.0
|
1.0
|
CG2
|
D:ILE527
|
3.2
|
27.5
|
1.0
|
C2
|
D:VQP801
|
3.6
|
26.7
|
1.0
|
C6
|
D:VQP801
|
3.6
|
28.5
|
1.0
|
C23
|
D:VQP801
|
3.7
|
29.7
|
1.0
|
CB
|
D:ILE527
|
3.8
|
28.9
|
1.0
|
CD
|
D:GLU501
|
3.9
|
33.4
|
1.0
|
OE2
|
D:GLU501
|
3.9
|
36.9
|
1.0
|
CD1
|
D:ILE527
|
3.9
|
29.2
|
1.0
|
C7
|
D:VQP801
|
4.1
|
26.8
|
1.0
|
CG2
|
D:THR529
|
4.1
|
22.6
|
1.0
|
CG
|
D:GLU501
|
4.2
|
32.8
|
1.0
|
CE
|
D:LYS483
|
4.2
|
28.6
|
1.0
|
OE1
|
D:GLU501
|
4.2
|
34.1
|
1.0
|
NZ
|
D:LYS483
|
4.4
|
31.4
|
1.0
|
N25
|
D:VQP801
|
4.4
|
28.4
|
1.0
|
O24
|
D:VQP801
|
4.5
|
27.2
|
1.0
|
CG1
|
D:ILE527
|
4.5
|
28.1
|
1.0
|
CG
|
D:LEU505
|
4.7
|
29.1
|
1.0
|
C1
|
D:VQP801
|
4.8
|
25.1
|
1.0
|
|
Reference:
M.P.Huestis,
D.Dela Cruz,
A.G.Dipasquale,
M.R.Durk,
C.Eigenbrot,
P.Gibbons,
A.Gobbi,
T.L.Hunsaker,
H.La,
D.H.Leung,
W.Liu,
S.Malek,
M.Merchant,
J.G.Moffat,
C.S.Muli,
C.J.Orr,
B.T.Parr,
F.Shanahan,
C.J.Sneeringer,
W.Wang,
I.Yen,
J.Yin,
M.Siu,
J.Rudolph.
Targeting Kras Mutant Cancers Via Combination Treatment: Discovery of A 5-Fluoro-4-(3 H )-Quinazolinone Aryl Urea Pan-Raf Kinase Inhibitor. J.Med.Chem. V. 64 3940 2021.
ISSN: ISSN 0022-2623
PubMed: 33780623
DOI: 10.1021/ACS.JMEDCHEM.0C02085
Page generated: Fri Aug 2 08:08:34 2024
|