Fluorine in PDB 6n3l: Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Enzymatic activity of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
All present enzymatic activity of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents:
2.7.11.1;
Protein crystallography data
The structure of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents, PDB code: 6n3l
was solved by
I.D.Hoffman,
J.Fujimoto,
O.Kurasawa,
T.Takagi,
M.G.Klein,
G.Kefala,
S.C.Ding,
D.R.Cary,
R.Mizojiri,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.61
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.886,
122.233,
120.674,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.3 /
29
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
(pdb code 6n3l). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents, PDB code: 6n3l:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 1 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2501
b:45.4
occ:1.00
|
F12
|
A:KAV2501
|
0.0
|
45.4
|
1.0
|
C11
|
A:KAV2501
|
1.4
|
47.0
|
1.0
|
F13
|
A:KAV2501
|
2.1
|
50.1
|
1.0
|
F14
|
A:KAV2501
|
2.2
|
50.2
|
1.0
|
C8
|
A:KAV2501
|
2.4
|
51.0
|
1.0
|
C9
|
A:KAV2501
|
3.2
|
47.1
|
1.0
|
C7
|
A:KAV2501
|
3.2
|
46.0
|
1.0
|
CD1
|
A:LEU643
|
3.3
|
45.0
|
1.0
|
CE
|
A:MET844
|
3.3
|
57.9
|
1.0
|
CG2
|
A:ILE839
|
3.8
|
52.8
|
1.0
|
CD1
|
A:ILE839
|
4.0
|
50.9
|
1.0
|
CG2
|
A:ILE648
|
4.3
|
37.1
|
1.0
|
CB
|
A:ILE839
|
4.4
|
45.2
|
1.0
|
C6
|
A:KAV2501
|
4.4
|
51.7
|
1.0
|
C10
|
A:KAV2501
|
4.4
|
49.4
|
1.0
|
CD1
|
A:ILE648
|
4.6
|
37.2
|
1.0
|
SD
|
A:MET844
|
4.6
|
64.4
|
1.0
|
CG
|
A:LEU643
|
4.7
|
50.9
|
1.0
|
CD2
|
A:LEU640
|
4.7
|
51.2
|
1.0
|
CG1
|
A:ILE839
|
4.8
|
48.1
|
1.0
|
C5
|
A:KAV2501
|
4.9
|
51.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 2 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2501
b:50.1
occ:1.00
|
F13
|
A:KAV2501
|
0.0
|
50.1
|
1.0
|
C11
|
A:KAV2501
|
1.3
|
47.0
|
1.0
|
F12
|
A:KAV2501
|
2.1
|
45.4
|
1.0
|
C8
|
A:KAV2501
|
2.2
|
51.0
|
1.0
|
F14
|
A:KAV2501
|
2.3
|
50.2
|
1.0
|
C9
|
A:KAV2501
|
2.5
|
47.1
|
1.0
|
C7
|
A:KAV2501
|
3.5
|
46.0
|
1.0
|
CD2
|
A:HIS846
|
3.5
|
49.1
|
1.0
|
CD1
|
A:ILE839
|
3.8
|
50.9
|
1.0
|
C10
|
A:KAV2501
|
3.9
|
49.4
|
1.0
|
CE
|
A:MET844
|
4.0
|
57.9
|
1.0
|
CG
|
A:HIS846
|
4.1
|
50.5
|
1.0
|
NE2
|
A:HIS846
|
4.2
|
48.6
|
1.0
|
CA
|
A:HIS846
|
4.4
|
45.2
|
1.0
|
CB
|
A:HIS846
|
4.4
|
47.0
|
1.0
|
C6
|
A:KAV2501
|
4.5
|
51.7
|
1.0
|
C5
|
A:KAV2501
|
4.7
|
51.6
|
1.0
|
ND1
|
A:HIS846
|
4.9
|
48.6
|
1.0
|
CG2
|
A:ILE864
|
5.0
|
40.1
|
1.0
|
CG1
|
A:ILE839
|
5.0
|
48.1
|
1.0
|
CE1
|
A:HIS846
|
5.0
|
55.2
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 3 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2501
b:50.2
occ:1.00
|
F14
|
A:KAV2501
|
0.0
|
50.2
|
1.0
|
C11
|
A:KAV2501
|
1.4
|
47.0
|
1.0
|
F12
|
A:KAV2501
|
2.2
|
45.4
|
1.0
|
F13
|
A:KAV2501
|
2.3
|
50.1
|
1.0
|
C8
|
A:KAV2501
|
2.4
|
51.0
|
1.0
|
C7
|
A:KAV2501
|
2.8
|
46.0
|
1.0
|
CG2
|
A:ILE864
|
3.5
|
40.1
|
1.0
|
C9
|
A:KAV2501
|
3.6
|
47.1
|
1.0
|
CD1
|
A:ILE648
|
3.7
|
37.2
|
1.0
|
CD1
|
A:ILE839
|
3.8
|
50.9
|
1.0
|
O
|
A:ILE864
|
3.8
|
40.4
|
1.0
|
CB
|
A:ILE864
|
4.0
|
39.8
|
1.0
|
CD2
|
A:HIS846
|
4.0
|
49.1
|
1.0
|
CG2
|
A:ILE648
|
4.1
|
37.1
|
1.0
|
C6
|
A:KAV2501
|
4.1
|
51.7
|
1.0
|
C
|
A:ILE864
|
4.2
|
39.4
|
1.0
|
CG2
|
A:ILE839
|
4.3
|
52.8
|
1.0
|
NE2
|
A:HIS846
|
4.5
|
48.6
|
1.0
|
N
|
A:GLY865
|
4.7
|
43.0
|
1.0
|
CA
|
A:ILE864
|
4.8
|
39.4
|
1.0
|
C10
|
A:KAV2501
|
4.8
|
49.4
|
1.0
|
CG1
|
A:ILE648
|
4.9
|
38.5
|
1.0
|
CA
|
A:GLY865
|
4.9
|
42.6
|
1.0
|
O
|
A:GLY865
|
5.0
|
42.5
|
1.0
|
CD1
|
A:LEU643
|
5.0
|
45.0
|
1.0
|
C5
|
A:KAV2501
|
5.0
|
51.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 4 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2501
b:47.8
occ:1.00
|
F12
|
B:KAV2501
|
0.0
|
47.8
|
1.0
|
C11
|
B:KAV2501
|
1.4
|
47.9
|
1.0
|
F14
|
B:KAV2501
|
2.2
|
49.8
|
1.0
|
F13
|
B:KAV2501
|
2.3
|
41.1
|
1.0
|
C8
|
B:KAV2501
|
2.3
|
50.5
|
1.0
|
C7
|
B:KAV2501
|
2.9
|
47.5
|
1.0
|
CD1
|
B:LEU643
|
3.2
|
51.7
|
1.0
|
C9
|
B:KAV2501
|
3.4
|
50.2
|
1.0
|
CG2
|
B:ILE648
|
3.5
|
45.9
|
1.0
|
CG2
|
B:ILE839
|
3.7
|
53.2
|
1.0
|
CD1
|
B:ILE648
|
4.0
|
40.9
|
1.0
|
C6
|
B:KAV2501
|
4.1
|
48.5
|
1.0
|
CE
|
B:MET844
|
4.2
|
64.8
|
1.0
|
CD1
|
B:ILE839
|
4.3
|
53.6
|
1.0
|
C10
|
B:KAV2501
|
4.6
|
50.5
|
1.0
|
CB
|
B:ILE839
|
4.6
|
50.7
|
1.0
|
CG
|
B:LEU643
|
4.6
|
54.4
|
1.0
|
CG1
|
B:ILE648
|
4.7
|
42.5
|
1.0
|
CB
|
B:ILE648
|
4.7
|
42.7
|
1.0
|
CD2
|
B:LEU640
|
4.7
|
59.5
|
1.0
|
C5
|
B:KAV2501
|
4.9
|
51.2
|
1.0
|
SD
|
B:MET844
|
5.0
|
66.2
|
1.0
|
O
|
B:ILE864
|
5.0
|
40.3
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 5 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2501
b:41.1
occ:1.00
|
F13
|
B:KAV2501
|
0.0
|
41.1
|
1.0
|
C11
|
B:KAV2501
|
1.4
|
47.9
|
1.0
|
F14
|
B:KAV2501
|
2.2
|
49.8
|
1.0
|
C8
|
B:KAV2501
|
2.2
|
50.5
|
1.0
|
F12
|
B:KAV2501
|
2.3
|
47.8
|
1.0
|
C9
|
B:KAV2501
|
2.5
|
50.2
|
1.0
|
CE
|
B:MET844
|
3.4
|
64.8
|
1.0
|
C7
|
B:KAV2501
|
3.5
|
47.5
|
1.0
|
CD2
|
B:HIS846
|
3.8
|
42.2
|
1.0
|
C10
|
B:KAV2501
|
3.8
|
50.5
|
1.0
|
CD1
|
B:ILE839
|
3.9
|
53.6
|
1.0
|
CG
|
B:HIS846
|
4.3
|
42.8
|
1.0
|
CA
|
B:HIS846
|
4.5
|
42.0
|
1.0
|
NE2
|
B:HIS846
|
4.5
|
41.8
|
1.0
|
C6
|
B:KAV2501
|
4.6
|
48.5
|
1.0
|
CB
|
B:HIS846
|
4.6
|
43.3
|
1.0
|
CD1
|
B:LEU643
|
4.7
|
51.7
|
1.0
|
C5
|
B:KAV2501
|
4.7
|
51.2
|
1.0
|
CG2
|
B:ILE839
|
4.7
|
53.2
|
1.0
|
SD
|
B:MET844
|
4.9
|
66.2
|
1.0
|
CB
|
B:ILE839
|
5.0
|
50.7
|
1.0
|
CG1
|
B:ILE839
|
5.0
|
51.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6n3l
Go back to
Fluorine Binding Sites List in 6n3l
Fluorine binding site 6 out
of 6 in the Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Identification of Novel, Potent and Selective GCN2 Inhibitors As First-in-Class Anti-Tumor Agents within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2501
b:49.8
occ:1.00
|
F14
|
B:KAV2501
|
0.0
|
49.8
|
1.0
|
C11
|
B:KAV2501
|
1.4
|
47.9
|
1.0
|
F12
|
B:KAV2501
|
2.2
|
47.8
|
1.0
|
F13
|
B:KAV2501
|
2.2
|
41.1
|
1.0
|
C8
|
B:KAV2501
|
2.5
|
50.5
|
1.0
|
CD2
|
B:HIS846
|
3.2
|
42.2
|
1.0
|
C7
|
B:KAV2501
|
3.2
|
47.5
|
1.0
|
CG2
|
B:ILE864
|
3.4
|
42.3
|
1.0
|
C9
|
B:KAV2501
|
3.5
|
50.2
|
1.0
|
CD1
|
B:ILE839
|
3.6
|
53.6
|
1.0
|
NE2
|
B:HIS846
|
3.9
|
41.8
|
1.0
|
CB
|
B:ILE864
|
4.1
|
44.6
|
1.0
|
CD1
|
B:ILE648
|
4.1
|
40.9
|
1.0
|
CG
|
B:HIS846
|
4.2
|
42.8
|
1.0
|
O
|
B:ILE864
|
4.3
|
40.3
|
1.0
|
CG2
|
B:ILE839
|
4.4
|
53.2
|
1.0
|
C
|
B:ILE864
|
4.5
|
40.9
|
1.0
|
C6
|
B:KAV2501
|
4.5
|
48.5
|
1.0
|
CG2
|
B:ILE648
|
4.6
|
45.9
|
1.0
|
C10
|
B:KAV2501
|
4.7
|
50.5
|
1.0
|
CB
|
B:HIS846
|
4.8
|
43.3
|
1.0
|
O
|
B:GLY865
|
4.8
|
45.7
|
1.0
|
N
|
B:GLY865
|
4.9
|
41.3
|
1.0
|
CG1
|
B:ILE839
|
4.9
|
51.3
|
1.0
|
CA
|
B:ILE864
|
4.9
|
45.3
|
1.0
|
CA
|
B:GLY865
|
5.0
|
44.0
|
1.0
|
|
Reference:
J.Fujimoto,
O.Kurasawa,
T.Takagi,
X.Liu,
H.Banno,
T.Kojima,
Y.Asano,
A.Nakamura,
T.Nambu,
A.Hata,
T.Ishii,
T.Sameshima,
Y.Debori,
M.Miyamoto,
M.G.Klein,
R.Tjhen,
B.C.Sang,
I.Levin,
S.W.Lane,
G.P.Snell,
K.Li,
G.Kefala,
I.D.Hoffman,
S.C.Ding,
D.R.Cary,
R.Mizojiri.
Identification of Novel, Potent, and Orally Available GCN2 Inhibitors with Type I Half Binding Mode. Acs Med.Chem.Lett. V. 10 1498 2019.
ISSN: ISSN 1948-5875
PubMed: 31620240
DOI: 10.1021/ACSMEDCHEMLETT.9B00400
Page generated: Thu Aug 1 22:26:17 2024
|