Fluorine in PDB 6duk: Egfr with An Allosteric Inhibitor
Enzymatic activity of Egfr with An Allosteric Inhibitor
All present enzymatic activity of Egfr with An Allosteric Inhibitor:
2.7.10.1;
Protein crystallography data
The structure of Egfr with An Allosteric Inhibitor, PDB code: 6duk
was solved by
E.Park,
M.J.Eck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
88.50 /
2.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.481,
94.711,
97.398,
70.38,
77.46,
79.14
|
R / Rfree (%)
|
19 /
22.3
|
Other elements in 6duk:
The structure of Egfr with An Allosteric Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Egfr with An Allosteric Inhibitor
(pdb code 6duk). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Egfr with An Allosteric Inhibitor, PDB code: 6duk:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 1 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1103
b:26.7
occ:1.00
|
F35
|
A:JBJ1103
|
0.0
|
26.7
|
1.0
|
C34
|
A:JBJ1103
|
1.4
|
24.4
|
1.0
|
C36
|
A:JBJ1103
|
2.4
|
23.9
|
1.0
|
C33
|
A:JBJ1103
|
2.4
|
20.1
|
1.0
|
C
|
A:ARG776
|
2.9
|
22.8
|
1.0
|
N
|
A:LEU777
|
2.9
|
25.0
|
1.0
|
O
|
A:ARG776
|
3.0
|
26.0
|
1.0
|
CA
|
A:LEU777
|
3.4
|
24.7
|
1.0
|
O
|
A:CYS775
|
3.5
|
24.4
|
1.0
|
CA
|
A:ARG776
|
3.6
|
26.4
|
1.0
|
C37
|
A:JBJ1103
|
3.6
|
25.3
|
1.0
|
C
|
A:CYS775
|
3.6
|
27.7
|
1.0
|
C32
|
A:JBJ1103
|
3.7
|
26.2
|
1.0
|
N
|
A:ARG776
|
3.7
|
26.9
|
1.0
|
CB
|
A:CYS775
|
3.9
|
24.7
|
1.0
|
CB
|
A:LEU777
|
4.0
|
21.5
|
1.0
|
C38
|
A:JBJ1103
|
4.1
|
21.7
|
1.0
|
CE
|
A:MET790
|
4.1
|
22.7
|
1.0
|
SD
|
A:MET790
|
4.3
|
25.7
|
1.0
|
CB
|
A:MET790
|
4.3
|
26.1
|
1.0
|
CA
|
A:CYS775
|
4.5
|
25.9
|
1.0
|
OG1
|
A:THR854
|
4.5
|
23.5
|
1.0
|
O
|
A:HOH1245
|
4.7
|
21.2
|
1.0
|
C
|
A:LEU777
|
4.8
|
26.6
|
1.0
|
C09
|
A:JBJ1103
|
4.9
|
24.1
|
1.0
|
C02
|
A:JBJ1103
|
4.9
|
25.3
|
1.0
|
CD1
|
A:LEU777
|
5.0
|
23.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 2 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1103
b:37.1
occ:1.00
|
F35
|
B:JBJ1103
|
0.0
|
37.1
|
1.0
|
C34
|
B:JBJ1103
|
1.3
|
35.2
|
1.0
|
C33
|
B:JBJ1103
|
2.3
|
35.5
|
1.0
|
C36
|
B:JBJ1103
|
2.3
|
38.7
|
1.0
|
N
|
B:LEU777
|
3.0
|
30.5
|
1.0
|
C
|
B:ARG776
|
3.0
|
30.8
|
1.0
|
O
|
B:ARG776
|
3.2
|
28.5
|
1.0
|
CA
|
B:LEU777
|
3.4
|
34.7
|
1.0
|
C32
|
B:JBJ1103
|
3.6
|
37.0
|
1.0
|
C37
|
B:JBJ1103
|
3.6
|
37.6
|
1.0
|
CA
|
B:ARG776
|
3.7
|
29.4
|
1.0
|
CE
|
B:MET790
|
3.8
|
28.3
|
1.0
|
N
|
B:ARG776
|
3.8
|
29.6
|
1.0
|
C
|
B:CYS775
|
3.9
|
34.2
|
1.0
|
O
|
B:CYS775
|
3.9
|
28.6
|
1.0
|
SD
|
B:MET790
|
4.0
|
36.7
|
1.0
|
CB
|
B:MET790
|
4.0
|
33.8
|
1.0
|
C38
|
B:JBJ1103
|
4.1
|
38.8
|
1.0
|
CB
|
B:LEU777
|
4.1
|
28.3
|
1.0
|
CB
|
B:CYS775
|
4.1
|
32.1
|
1.0
|
CD1
|
B:LEU777
|
4.5
|
29.8
|
1.0
|
OG1
|
B:THR854
|
4.6
|
26.9
|
1.0
|
CG
|
B:MET790
|
4.6
|
30.3
|
1.0
|
C02
|
B:JBJ1103
|
4.7
|
38.2
|
1.0
|
CA
|
B:CYS775
|
4.7
|
28.9
|
1.0
|
C09
|
B:JBJ1103
|
4.7
|
38.2
|
1.0
|
C
|
B:LEU777
|
4.7
|
31.8
|
1.0
|
O
|
B:HOH1243
|
4.9
|
27.2
|
1.0
|
O01
|
B:JBJ1103
|
4.9
|
40.8
|
1.0
|
CG
|
B:LEU777
|
5.0
|
33.0
|
1.0
|
N03
|
B:JBJ1103
|
5.0
|
39.2
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 3 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1103
b:29.4
occ:1.00
|
F35
|
C:JBJ1103
|
0.0
|
29.4
|
1.0
|
C34
|
C:JBJ1103
|
1.4
|
33.9
|
1.0
|
C36
|
C:JBJ1103
|
2.4
|
34.6
|
1.0
|
C33
|
C:JBJ1103
|
2.4
|
30.4
|
1.0
|
C
|
C:ARG776
|
3.1
|
28.2
|
1.0
|
N
|
C:LEU777
|
3.1
|
28.3
|
1.0
|
O
|
C:ARG776
|
3.3
|
28.6
|
1.0
|
CA
|
C:LEU777
|
3.5
|
27.1
|
1.0
|
C37
|
C:JBJ1103
|
3.6
|
35.4
|
1.0
|
C32
|
C:JBJ1103
|
3.7
|
34.9
|
1.0
|
O
|
C:CYS775
|
3.8
|
32.6
|
1.0
|
N
|
C:ARG776
|
3.8
|
37.3
|
1.0
|
C
|
C:CYS775
|
3.8
|
31.4
|
1.0
|
CE
|
C:MET790
|
3.8
|
27.0
|
1.0
|
CA
|
C:ARG776
|
3.9
|
30.5
|
1.0
|
CB
|
C:LEU777
|
4.0
|
30.1
|
1.0
|
CB
|
C:CYS775
|
4.1
|
33.8
|
1.0
|
SD
|
C:MET790
|
4.1
|
31.4
|
1.0
|
C38
|
C:JBJ1103
|
4.1
|
37.6
|
1.0
|
CB
|
C:MET790
|
4.2
|
29.5
|
1.0
|
OG1
|
C:THR854
|
4.4
|
27.8
|
1.0
|
CA
|
C:CYS775
|
4.6
|
34.2
|
1.0
|
O
|
C:HOH1222
|
4.8
|
26.5
|
1.0
|
CG
|
C:MET790
|
4.8
|
27.4
|
1.0
|
C
|
C:LEU777
|
4.9
|
32.4
|
1.0
|
C09
|
C:JBJ1103
|
4.9
|
35.1
|
1.0
|
C02
|
C:JBJ1103
|
4.9
|
35.5
|
1.0
|
CD1
|
C:LEU777
|
5.0
|
30.7
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 4 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1103
b:27.9
occ:1.00
|
F35
|
D:JBJ1103
|
0.0
|
27.9
|
1.0
|
C34
|
D:JBJ1103
|
1.3
|
23.3
|
1.0
|
C36
|
D:JBJ1103
|
2.3
|
23.7
|
1.0
|
C33
|
D:JBJ1103
|
2.3
|
24.7
|
1.0
|
N
|
D:LEU777
|
3.1
|
21.2
|
1.0
|
C
|
D:ARG776
|
3.1
|
23.9
|
1.0
|
O
|
D:ARG776
|
3.3
|
24.0
|
1.0
|
CA
|
D:LEU777
|
3.4
|
26.0
|
1.0
|
C37
|
D:JBJ1103
|
3.5
|
26.5
|
1.0
|
C32
|
D:JBJ1103
|
3.6
|
25.4
|
1.0
|
CE
|
D:MET790
|
3.7
|
18.1
|
1.0
|
O
|
D:CYS775
|
3.9
|
25.1
|
1.0
|
CA
|
D:ARG776
|
3.9
|
21.6
|
1.0
|
C
|
D:CYS775
|
3.9
|
30.6
|
1.0
|
N
|
D:ARG776
|
3.9
|
22.3
|
1.0
|
CB
|
D:LEU777
|
4.0
|
26.0
|
1.0
|
CB
|
D:CYS775
|
4.0
|
22.4
|
1.0
|
SD
|
D:MET790
|
4.0
|
27.3
|
1.0
|
C38
|
D:JBJ1103
|
4.0
|
27.3
|
1.0
|
CB
|
D:MET790
|
4.2
|
22.5
|
1.0
|
OG1
|
D:THR854
|
4.4
|
25.2
|
1.0
|
CA
|
D:CYS775
|
4.6
|
22.3
|
1.0
|
O
|
D:HOH1222
|
4.7
|
23.9
|
1.0
|
C02
|
D:JBJ1103
|
4.7
|
25.6
|
1.0
|
C09
|
D:JBJ1103
|
4.8
|
26.6
|
1.0
|
CD1
|
D:LEU777
|
4.8
|
21.3
|
1.0
|
CG
|
D:MET790
|
4.8
|
20.9
|
1.0
|
C
|
D:LEU777
|
4.8
|
27.0
|
1.0
|
O01
|
D:JBJ1103
|
5.0
|
25.9
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 5 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F1103
b:28.9
occ:1.00
|
F35
|
E:JBJ1103
|
0.0
|
28.9
|
1.0
|
C34
|
E:JBJ1103
|
1.3
|
31.5
|
1.0
|
C36
|
E:JBJ1103
|
2.4
|
32.5
|
1.0
|
C33
|
E:JBJ1103
|
2.4
|
27.5
|
1.0
|
C
|
E:ARG776
|
3.0
|
25.3
|
1.0
|
N
|
E:LEU777
|
3.0
|
27.9
|
1.0
|
O
|
E:ARG776
|
3.2
|
26.6
|
1.0
|
CA
|
E:LEU777
|
3.4
|
27.2
|
1.0
|
C37
|
E:JBJ1103
|
3.6
|
29.6
|
1.0
|
CA
|
E:ARG776
|
3.6
|
30.5
|
1.0
|
C32
|
E:JBJ1103
|
3.7
|
34.0
|
1.0
|
O
|
E:CYS775
|
3.7
|
27.4
|
1.0
|
N
|
E:ARG776
|
3.8
|
31.2
|
1.0
|
C
|
E:CYS775
|
3.8
|
29.9
|
1.0
|
CB
|
E:LEU777
|
3.9
|
28.7
|
1.0
|
CE
|
E:MET790
|
4.0
|
29.0
|
1.0
|
CB
|
E:CYS775
|
4.0
|
31.3
|
1.0
|
SD
|
E:MET790
|
4.0
|
32.0
|
1.0
|
C38
|
E:JBJ1103
|
4.1
|
31.5
|
1.0
|
CB
|
E:MET790
|
4.3
|
26.3
|
1.0
|
OG1
|
E:THR854
|
4.5
|
27.3
|
1.0
|
CA
|
E:CYS775
|
4.6
|
30.1
|
1.0
|
O
|
E:HOH1210
|
4.7
|
25.4
|
1.0
|
CD1
|
E:LEU777
|
4.7
|
23.8
|
1.0
|
C
|
E:LEU777
|
4.8
|
30.9
|
1.0
|
C09
|
E:JBJ1103
|
4.8
|
31.3
|
1.0
|
CG
|
E:MET790
|
4.9
|
28.6
|
1.0
|
C02
|
E:JBJ1103
|
4.9
|
30.2
|
1.0
|
CG
|
E:LEU777
|
5.0
|
31.7
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6duk
Go back to
Fluorine Binding Sites List in 6duk
Fluorine binding site 6 out
of 6 in the Egfr with An Allosteric Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F1103
b:30.8
occ:1.00
|
F35
|
F:JBJ1103
|
0.0
|
30.8
|
1.0
|
C34
|
F:JBJ1103
|
1.5
|
31.5
|
1.0
|
C33
|
F:JBJ1103
|
2.5
|
34.1
|
1.0
|
C36
|
F:JBJ1103
|
2.5
|
29.7
|
1.0
|
N
|
F:LEU777
|
2.9
|
27.2
|
1.0
|
C
|
F:ARG776
|
3.0
|
26.3
|
1.0
|
O
|
F:ARG776
|
3.2
|
23.3
|
1.0
|
CA
|
F:LEU777
|
3.3
|
31.5
|
1.0
|
CE
|
F:MET790
|
3.6
|
26.4
|
1.0
|
O
|
F:CYS775
|
3.7
|
28.6
|
1.0
|
C32
|
F:JBJ1103
|
3.8
|
32.0
|
1.0
|
C37
|
F:JBJ1103
|
3.8
|
31.6
|
1.0
|
CA
|
F:ARG776
|
3.8
|
28.8
|
1.0
|
C
|
F:CYS775
|
3.8
|
27.7
|
1.0
|
CB
|
F:CYS775
|
3.9
|
31.2
|
1.0
|
N
|
F:ARG776
|
3.9
|
30.3
|
1.0
|
CB
|
F:LEU777
|
4.0
|
27.6
|
1.0
|
SD
|
F:MET790
|
4.0
|
30.1
|
1.0
|
CB
|
F:MET790
|
4.1
|
29.8
|
1.0
|
C38
|
F:JBJ1103
|
4.2
|
33.1
|
1.0
|
CA
|
F:CYS775
|
4.5
|
25.7
|
1.0
|
OG1
|
F:THR854
|
4.6
|
28.4
|
1.0
|
C
|
F:LEU777
|
4.7
|
30.9
|
1.0
|
CG
|
F:MET790
|
4.7
|
29.4
|
1.0
|
O
|
F:HOH1225
|
4.7
|
28.5
|
1.0
|
CD1
|
F:LEU777
|
4.8
|
28.3
|
1.0
|
C02
|
F:JBJ1103
|
4.8
|
35.7
|
1.0
|
C09
|
F:JBJ1103
|
4.9
|
33.0
|
1.0
|
O01
|
F:JBJ1103
|
4.9
|
35.2
|
1.0
|
|
Reference:
C.To,
J.Jang,
T.Chen,
E.Park,
M.Mushajiang,
D.J.H.De Clercq,
M.Xu,
S.Wang,
M.D.Cameron,
D.E.Heppner,
B.H.Shin,
T.W.Gero,
A.Yang,
S.E.Dahlberg,
K.K.Wong,
M.J.Eck,
N.S.Gray,
P.A.Janne.
Single and Dual Targeting of Mutant Egfr with An Allosteric Inhibitor. Cancer Discov V. 9 926 2019.
ISSN: ESSN 2159-8290
PubMed: 31092401
DOI: 10.1158/2159-8290.CD-18-0903
Page generated: Thu Aug 1 19:11:31 2024
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