Fluorine in PDB 6eg9: IRAK4 in Complex with Ponatinib
Enzymatic activity of IRAK4 in Complex with Ponatinib
All present enzymatic activity of IRAK4 in Complex with Ponatinib:
2.7.11.1;
Protein crystallography data
The structure of IRAK4 in Complex with Ponatinib, PDB code: 6eg9
was solved by
L.Wang,
H.Wu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.61 /
2.41
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.037,
85.037,
434.301,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.3 /
24.9
|
Other elements in 6eg9:
The structure of IRAK4 in Complex with Ponatinib also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the IRAK4 in Complex with Ponatinib
(pdb code 6eg9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
IRAK4 in Complex with Ponatinib, PDB code: 6eg9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 1 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:59.4
occ:1.00
|
F1
|
A:0LI501
|
0.0
|
59.4
|
1.0
|
C19
|
A:0LI501
|
1.3
|
60.7
|
1.0
|
F2
|
A:0LI501
|
1.9
|
60.2
|
1.0
|
F3
|
A:0LI501
|
1.9
|
58.8
|
1.0
|
C17
|
A:0LI501
|
2.1
|
52.5
|
1.0
|
C18
|
A:0LI501
|
2.4
|
48.0
|
1.0
|
O
|
A:ILE327
|
3.0
|
51.9
|
1.0
|
C16
|
A:0LI501
|
3.4
|
49.3
|
1.0
|
CG2
|
A:VAL246
|
3.7
|
59.9
|
1.0
|
C
|
A:ILE327
|
3.8
|
48.5
|
1.0
|
C13
|
A:0LI501
|
3.8
|
52.6
|
1.0
|
CA
|
A:SER328
|
3.8
|
51.6
|
1.0
|
O1
|
A:0LI501
|
4.1
|
52.1
|
1.0
|
C20
|
A:0LI501
|
4.1
|
53.7
|
1.0
|
N
|
A:SER328
|
4.2
|
49.6
|
1.0
|
C
|
A:SER328
|
4.2
|
53.2
|
1.0
|
N
|
A:ASP329
|
4.3
|
51.9
|
1.0
|
CB
|
A:LEU245
|
4.4
|
53.2
|
1.0
|
CD2
|
A:LEU245
|
4.4
|
61.5
|
1.0
|
N
|
A:VAL246
|
4.5
|
56.1
|
1.0
|
C15
|
A:0LI501
|
4.5
|
46.3
|
1.0
|
CG2
|
A:ILE327
|
4.5
|
48.0
|
1.0
|
C14
|
A:0LI501
|
4.6
|
52.0
|
1.0
|
SD
|
A:MET237
|
4.7
|
73.9
|
1.0
|
N2
|
A:0LI501
|
4.7
|
53.1
|
1.0
|
CD1
|
A:LEU245
|
4.7
|
65.4
|
1.0
|
CG
|
A:LEU245
|
4.8
|
61.4
|
1.0
|
O
|
A:VAL246
|
4.8
|
61.5
|
1.0
|
C12
|
A:0LI501
|
4.8
|
55.5
|
1.0
|
O
|
A:SER328
|
4.8
|
52.0
|
1.0
|
CE
|
A:MET237
|
4.9
|
65.1
|
1.0
|
CA
|
A:LEU245
|
4.9
|
53.5
|
1.0
|
CB
|
A:ILE327
|
4.9
|
51.5
|
1.0
|
CA
|
A:ILE327
|
4.9
|
46.2
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 2 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:60.2
occ:1.00
|
F2
|
A:0LI501
|
0.0
|
60.2
|
1.0
|
C19
|
A:0LI501
|
1.1
|
60.7
|
1.0
|
F3
|
A:0LI501
|
1.9
|
58.8
|
1.0
|
F1
|
A:0LI501
|
1.9
|
59.4
|
1.0
|
C17
|
A:0LI501
|
2.2
|
52.5
|
1.0
|
C16
|
A:0LI501
|
2.9
|
49.3
|
1.0
|
C20
|
A:0LI501
|
2.9
|
53.7
|
1.0
|
C18
|
A:0LI501
|
3.3
|
48.0
|
1.0
|
CD2
|
A:LEU302
|
3.8
|
52.4
|
1.0
|
CD1
|
A:LEU245
|
3.8
|
65.4
|
1.0
|
C15
|
A:0LI501
|
4.2
|
46.3
|
1.0
|
CD2
|
A:LEU245
|
4.3
|
61.5
|
1.0
|
CB
|
A:CYS240
|
4.3
|
66.6
|
1.0
|
CD1
|
A:LEU302
|
4.3
|
59.2
|
1.0
|
N3
|
A:0LI501
|
4.3
|
56.3
|
1.0
|
CG
|
A:LEU245
|
4.4
|
61.4
|
1.0
|
CG
|
A:LEU302
|
4.5
|
58.8
|
1.0
|
C13
|
A:0LI501
|
4.5
|
52.6
|
1.0
|
SG
|
A:CYS240
|
4.5
|
85.8
|
1.0
|
O
|
A:ILE327
|
4.6
|
51.9
|
1.0
|
CB
|
A:LEU245
|
4.6
|
53.2
|
1.0
|
SD
|
A:MET237
|
4.7
|
73.9
|
1.0
|
C14
|
A:0LI501
|
4.8
|
52.0
|
1.0
|
C21
|
A:0LI501
|
4.9
|
51.5
|
1.0
|
C24
|
A:0LI501
|
5.0
|
58.5
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 3 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:58.8
occ:1.00
|
F3
|
A:0LI501
|
0.0
|
58.8
|
1.0
|
C19
|
A:0LI501
|
1.1
|
60.7
|
1.0
|
F2
|
A:0LI501
|
1.9
|
60.2
|
1.0
|
F1
|
A:0LI501
|
1.9
|
59.4
|
1.0
|
C17
|
A:0LI501
|
2.1
|
52.5
|
1.0
|
C16
|
A:0LI501
|
3.0
|
49.3
|
1.0
|
C18
|
A:0LI501
|
3.1
|
48.0
|
1.0
|
C20
|
A:0LI501
|
3.1
|
53.7
|
1.0
|
CD2
|
A:HIS309
|
3.7
|
56.4
|
1.0
|
CG2
|
A:ILE327
|
3.8
|
48.0
|
1.0
|
NE2
|
A:HIS309
|
3.9
|
60.4
|
1.0
|
CD1
|
A:LEU302
|
4.0
|
59.2
|
1.0
|
O
|
A:ILE327
|
4.1
|
51.9
|
1.0
|
C
|
A:SER328
|
4.1
|
53.2
|
1.0
|
N3
|
A:0LI501
|
4.2
|
56.3
|
1.0
|
C21
|
A:0LI501
|
4.2
|
51.5
|
1.0
|
C15
|
A:0LI501
|
4.2
|
46.3
|
1.0
|
N
|
A:ASP329
|
4.3
|
51.9
|
1.0
|
O
|
A:SER328
|
4.3
|
52.0
|
1.0
|
C13
|
A:0LI501
|
4.4
|
52.6
|
1.0
|
C
|
A:ILE327
|
4.4
|
48.5
|
1.0
|
CB
|
A:ASP329
|
4.4
|
55.5
|
1.0
|
CA
|
A:SER328
|
4.4
|
51.6
|
1.0
|
CD2
|
A:LEU302
|
4.5
|
52.4
|
1.0
|
N
|
A:SER328
|
4.5
|
49.6
|
1.0
|
CD2
|
A:LEU245
|
4.7
|
61.5
|
1.0
|
CG
|
A:LEU302
|
4.8
|
58.8
|
1.0
|
CB
|
A:ILE327
|
4.8
|
51.5
|
1.0
|
C14
|
A:0LI501
|
4.8
|
52.0
|
1.0
|
CG
|
A:HIS309
|
4.8
|
62.4
|
1.0
|
CE1
|
A:HIS309
|
4.9
|
57.0
|
1.0
|
CA
|
A:ASP329
|
5.0
|
51.8
|
1.0
|
C24
|
A:0LI501
|
5.0
|
58.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 4 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:59.2
occ:1.00
|
F1
|
B:0LI501
|
0.0
|
59.2
|
1.0
|
C19
|
B:0LI501
|
1.3
|
68.4
|
1.0
|
F3
|
B:0LI501
|
1.9
|
60.5
|
1.0
|
F2
|
B:0LI501
|
1.9
|
67.8
|
1.0
|
C17
|
B:0LI501
|
2.1
|
57.0
|
1.0
|
C18
|
B:0LI501
|
2.4
|
47.0
|
1.0
|
O
|
B:ILE327
|
3.3
|
49.3
|
1.0
|
CG2
|
B:VAL246
|
3.3
|
56.4
|
1.0
|
C16
|
B:0LI501
|
3.5
|
56.0
|
1.0
|
CA
|
B:SER328
|
3.8
|
51.8
|
1.0
|
C13
|
B:0LI501
|
3.8
|
54.1
|
1.0
|
C
|
B:ILE327
|
3.8
|
48.0
|
1.0
|
CE
|
B:MET237
|
3.9
|
71.8
|
1.0
|
N
|
B:SER328
|
4.1
|
46.2
|
1.0
|
C
|
B:SER328
|
4.1
|
52.3
|
1.0
|
C20
|
B:0LI501
|
4.2
|
55.8
|
1.0
|
SD
|
B:MET237
|
4.2
|
69.1
|
1.0
|
O1
|
B:0LI501
|
4.2
|
56.0
|
1.0
|
N
|
B:ASP329
|
4.4
|
51.5
|
1.0
|
CG2
|
B:ILE327
|
4.4
|
45.9
|
1.0
|
C15
|
B:0LI501
|
4.5
|
55.0
|
1.0
|
N
|
B:VAL246
|
4.5
|
53.9
|
1.0
|
CD2
|
B:LEU245
|
4.5
|
47.6
|
1.0
|
CB
|
B:LEU245
|
4.6
|
51.1
|
1.0
|
CD1
|
B:LEU245
|
4.6
|
59.9
|
1.0
|
O
|
B:SER328
|
4.6
|
43.9
|
1.0
|
C14
|
B:0LI501
|
4.6
|
57.0
|
1.0
|
N2
|
B:0LI501
|
4.7
|
55.5
|
1.0
|
CB
|
B:VAL246
|
4.8
|
49.3
|
1.0
|
CB
|
B:ILE327
|
4.8
|
50.9
|
1.0
|
CG
|
B:LEU245
|
4.8
|
52.0
|
1.0
|
C12
|
B:0LI501
|
4.8
|
56.1
|
1.0
|
CA
|
B:ILE327
|
4.9
|
43.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 5 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:67.8
occ:1.00
|
F2
|
B:0LI501
|
0.0
|
67.8
|
1.0
|
C19
|
B:0LI501
|
1.1
|
68.4
|
1.0
|
F3
|
B:0LI501
|
1.9
|
60.5
|
1.0
|
F1
|
B:0LI501
|
1.9
|
59.2
|
1.0
|
C17
|
B:0LI501
|
2.2
|
57.0
|
1.0
|
C16
|
B:0LI501
|
2.9
|
56.0
|
1.0
|
C20
|
B:0LI501
|
2.9
|
55.8
|
1.0
|
C18
|
B:0LI501
|
3.3
|
47.0
|
1.0
|
CD2
|
B:LEU302
|
3.6
|
54.0
|
1.0
|
SD
|
B:MET237
|
3.8
|
69.1
|
1.0
|
CD1
|
B:LEU245
|
3.9
|
59.9
|
1.0
|
N3
|
B:0LI501
|
3.9
|
60.2
|
1.0
|
CD1
|
B:LEU302
|
4.1
|
49.6
|
1.0
|
C15
|
B:0LI501
|
4.2
|
55.0
|
1.0
|
CE
|
B:MET237
|
4.2
|
71.8
|
1.0
|
CG
|
B:LEU302
|
4.4
|
56.8
|
1.0
|
CD2
|
B:LEU245
|
4.5
|
47.6
|
1.0
|
C13
|
B:0LI501
|
4.5
|
54.1
|
1.0
|
CG
|
B:LEU245
|
4.6
|
52.0
|
1.0
|
C21
|
B:0LI501
|
4.9
|
58.2
|
1.0
|
C14
|
B:0LI501
|
4.9
|
57.0
|
1.0
|
CB
|
B:LEU245
|
4.9
|
51.1
|
1.0
|
O
|
B:ILE327
|
4.9
|
49.3
|
1.0
|
C24
|
B:0LI501
|
5.0
|
62.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6eg9
Go back to
Fluorine Binding Sites List in 6eg9
Fluorine binding site 6 out
of 6 in the IRAK4 in Complex with Ponatinib
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of IRAK4 in Complex with Ponatinib within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:60.5
occ:1.00
|
F3
|
B:0LI501
|
0.0
|
60.5
|
1.0
|
C19
|
B:0LI501
|
1.1
|
68.4
|
1.0
|
F2
|
B:0LI501
|
1.9
|
67.8
|
1.0
|
F1
|
B:0LI501
|
1.9
|
59.2
|
1.0
|
C17
|
B:0LI501
|
2.1
|
57.0
|
1.0
|
C18
|
B:0LI501
|
3.0
|
47.0
|
1.0
|
C16
|
B:0LI501
|
3.0
|
56.0
|
1.0
|
C20
|
B:0LI501
|
3.3
|
55.8
|
1.0
|
NE2
|
B:HIS309
|
3.6
|
61.2
|
1.0
|
CD2
|
B:HIS309
|
3.6
|
50.5
|
1.0
|
N3
|
B:0LI501
|
3.8
|
60.2
|
1.0
|
CG2
|
B:ILE327
|
3.9
|
45.9
|
1.0
|
C
|
B:SER328
|
4.0
|
52.3
|
1.0
|
O
|
B:SER328
|
4.0
|
43.9
|
1.0
|
CD1
|
B:LEU302
|
4.0
|
49.6
|
1.0
|
CB
|
B:ASP329
|
4.2
|
57.2
|
1.0
|
CA
|
B:SER328
|
4.3
|
51.8
|
1.0
|
C15
|
B:0LI501
|
4.3
|
55.0
|
1.0
|
C13
|
B:0LI501
|
4.3
|
54.1
|
1.0
|
N
|
B:ASP329
|
4.3
|
51.5
|
1.0
|
O
|
B:ILE327
|
4.4
|
49.3
|
1.0
|
C24
|
B:0LI501
|
4.4
|
62.6
|
1.0
|
N
|
B:SER328
|
4.5
|
46.2
|
1.0
|
C
|
B:ILE327
|
4.5
|
48.0
|
1.0
|
CE1
|
B:HIS309
|
4.6
|
55.9
|
1.0
|
CD2
|
B:LEU302
|
4.6
|
54.0
|
1.0
|
CG
|
B:HIS309
|
4.7
|
56.6
|
1.0
|
C14
|
B:0LI501
|
4.8
|
57.0
|
1.0
|
CB
|
B:ILE327
|
4.8
|
50.9
|
1.0
|
CA
|
B:ASP329
|
4.9
|
51.0
|
1.0
|
CG
|
B:LEU302
|
4.9
|
56.8
|
1.0
|
|
Reference:
L.Wang,
R.Ferrao,
Q.Li,
J.M.Hatcher,
H.G.Choi,
S.J.Buhrlage,
N.S.Gray,
H.Wu.
Conformational Flexibility and Inhibitor Binding to Unphosphorylated Interleukin-1 Receptor-Associated Kinase 4 (IRAK4). J.Biol.Chem. V. 294 4511 2019.
ISSN: ESSN 1083-351X
PubMed: 30679311
DOI: 10.1074/JBC.RA118.005428
Page generated: Thu Aug 1 19:33:50 2024
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