Fluorine in PDB 6ega: IRAK4 in Complex with A Type II Inhibitor
Enzymatic activity of IRAK4 in Complex with A Type II Inhibitor
All present enzymatic activity of IRAK4 in Complex with A Type II Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of IRAK4 in Complex with A Type II Inhibitor, PDB code: 6ega
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)
|
73.29 /
2.51
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.629,
84.629,
429.041,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23 /
26.7
|
Other elements in 6ega:
The structure of IRAK4 in Complex with A Type II Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the IRAK4 in Complex with A Type II Inhibitor
(pdb code 6ega). 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 A Type II Inhibitor, PDB code: 6ega:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 1 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:85.4
occ:1.00
|
FAC
|
A:J8A501
|
0.0
|
85.4
|
1.0
|
CBO
|
A:J8A501
|
1.4
|
80.5
|
1.0
|
FAD
|
A:J8A501
|
2.2
|
80.8
|
1.0
|
FAE
|
A:J8A501
|
2.2
|
82.8
|
1.0
|
CBJ
|
A:J8A501
|
2.3
|
78.8
|
1.0
|
CAU
|
A:J8A501
|
2.9
|
83.7
|
1.0
|
CBG
|
A:J8A501
|
2.9
|
81.0
|
1.0
|
CAN
|
A:J8A501
|
3.4
|
75.1
|
1.0
|
CD2
|
A:LEU302
|
3.7
|
75.3
|
1.0
|
NBN
|
A:J8A501
|
3.7
|
83.5
|
1.0
|
SD
|
A:MET237
|
3.8
|
0.7
|
1.0
|
CD1
|
A:LEU245
|
3.9
|
86.8
|
1.0
|
CD1
|
A:LEU302
|
4.2
|
72.1
|
1.0
|
CAJ
|
A:J8A501
|
4.2
|
85.6
|
1.0
|
CAT
|
A:J8A501
|
4.4
|
85.4
|
1.0
|
CD2
|
A:LEU245
|
4.5
|
76.3
|
1.0
|
CG
|
A:LEU302
|
4.5
|
79.1
|
1.0
|
CBD
|
A:J8A501
|
4.6
|
79.6
|
1.0
|
CG
|
A:LEU245
|
4.7
|
78.6
|
1.0
|
CAS
|
A:J8A501
|
4.9
|
83.5
|
1.0
|
CAI
|
A:J8A501
|
4.9
|
82.8
|
1.0
|
O
|
A:ILE327
|
5.0
|
66.3
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 2 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:80.8
occ:1.00
|
FAD
|
A:J8A501
|
0.0
|
80.8
|
1.0
|
CBO
|
A:J8A501
|
1.3
|
80.5
|
1.0
|
FAE
|
A:J8A501
|
2.2
|
82.8
|
1.0
|
FAC
|
A:J8A501
|
2.2
|
85.4
|
1.0
|
CBJ
|
A:J8A501
|
2.2
|
78.8
|
1.0
|
CBG
|
A:J8A501
|
3.0
|
81.0
|
1.0
|
CAN
|
A:J8A501
|
3.2
|
75.1
|
1.0
|
CAU
|
A:J8A501
|
3.2
|
83.7
|
1.0
|
NBN
|
A:J8A501
|
3.3
|
83.5
|
1.0
|
CD2
|
A:HIS309
|
3.5
|
74.7
|
1.0
|
NE2
|
A:HIS309
|
3.6
|
79.5
|
1.0
|
CB
|
A:ASP329
|
3.9
|
76.1
|
1.0
|
CD1
|
A:LEU302
|
4.0
|
72.1
|
1.0
|
C
|
A:SER328
|
4.1
|
71.6
|
1.0
|
CAS
|
A:J8A501
|
4.2
|
83.5
|
1.0
|
O
|
A:SER328
|
4.2
|
64.3
|
1.0
|
N
|
A:ASP329
|
4.2
|
68.9
|
1.0
|
CG2
|
A:ILE327
|
4.3
|
61.9
|
1.0
|
CAJ
|
A:J8A501
|
4.3
|
85.6
|
1.0
|
CE1
|
A:HIS309
|
4.3
|
73.9
|
1.0
|
CG
|
A:HIS309
|
4.4
|
71.8
|
1.0
|
CAT
|
A:J8A501
|
4.4
|
85.4
|
1.0
|
CBD
|
A:J8A501
|
4.4
|
79.6
|
1.0
|
CA
|
A:SER328
|
4.6
|
67.3
|
1.0
|
CA
|
A:ASP329
|
4.7
|
72.0
|
1.0
|
CD2
|
A:LEU302
|
4.7
|
75.3
|
1.0
|
O
|
A:ILE327
|
4.7
|
66.3
|
1.0
|
ND1
|
A:HIS309
|
4.8
|
67.5
|
1.0
|
CAI
|
A:J8A501
|
4.8
|
82.8
|
1.0
|
N
|
A:SER328
|
4.9
|
67.2
|
1.0
|
C
|
A:ILE327
|
4.9
|
67.3
|
1.0
|
CG
|
A:LEU302
|
5.0
|
79.1
|
1.0
|
CAO
|
A:J8A501
|
5.0
|
85.1
|
1.0
|
CG
|
A:ASP329
|
5.0
|
83.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 3 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:82.8
occ:1.00
|
FAE
|
A:J8A501
|
0.0
|
82.8
|
1.0
|
CBO
|
A:J8A501
|
1.4
|
80.5
|
1.0
|
FAD
|
A:J8A501
|
2.2
|
80.8
|
1.0
|
FAC
|
A:J8A501
|
2.2
|
85.4
|
1.0
|
CBJ
|
A:J8A501
|
2.2
|
78.8
|
1.0
|
CAN
|
A:J8A501
|
2.5
|
75.1
|
1.0
|
O
|
A:ILE327
|
3.1
|
66.3
|
1.0
|
CBG
|
A:J8A501
|
3.6
|
81.0
|
1.0
|
CA
|
A:SER328
|
3.6
|
67.3
|
1.0
|
C
|
A:ILE327
|
3.8
|
67.3
|
1.0
|
CG2
|
A:VAL246
|
3.8
|
71.5
|
1.0
|
C
|
A:SER328
|
3.9
|
71.6
|
1.0
|
CBD
|
A:J8A501
|
3.9
|
79.6
|
1.0
|
OAA
|
A:J8A501
|
4.0
|
69.2
|
1.0
|
N
|
A:SER328
|
4.0
|
67.2
|
1.0
|
N
|
A:ASP329
|
4.1
|
68.9
|
1.0
|
CAU
|
A:J8A501
|
4.3
|
83.7
|
1.0
|
CG2
|
A:ILE327
|
4.3
|
61.9
|
1.0
|
SD
|
A:MET237
|
4.3
|
0.7
|
1.0
|
CD2
|
A:LEU245
|
4.4
|
76.3
|
1.0
|
O
|
A:SER328
|
4.5
|
64.3
|
1.0
|
CAJ
|
A:J8A501
|
4.6
|
85.6
|
1.0
|
CD1
|
A:LEU245
|
4.7
|
86.8
|
1.0
|
CBB
|
A:J8A501
|
4.7
|
70.9
|
1.0
|
NAY
|
A:J8A501
|
4.8
|
77.3
|
1.0
|
CB
|
A:ASP329
|
4.8
|
76.1
|
1.0
|
CAI
|
A:J8A501
|
4.8
|
82.8
|
1.0
|
N
|
A:VAL246
|
4.8
|
69.4
|
1.0
|
CB
|
A:SER328
|
4.9
|
62.5
|
1.0
|
NE2
|
A:HIS309
|
4.9
|
79.5
|
1.0
|
CB
|
A:ILE327
|
4.9
|
73.6
|
1.0
|
CG
|
A:LEU245
|
4.9
|
78.6
|
1.0
|
CB
|
A:LEU245
|
4.9
|
75.4
|
1.0
|
NBN
|
A:J8A501
|
5.0
|
83.5
|
1.0
|
CA
|
A:ILE327
|
5.0
|
68.0
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 4 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:84.1
occ:1.00
|
FAC
|
B:J8A501
|
0.0
|
84.1
|
1.0
|
CBO
|
B:J8A501
|
1.3
|
77.8
|
1.0
|
FAD
|
B:J8A501
|
2.1
|
83.4
|
1.0
|
FAE
|
B:J8A501
|
2.2
|
80.8
|
1.0
|
CBJ
|
B:J8A501
|
2.3
|
78.4
|
1.0
|
CBG
|
B:J8A501
|
2.9
|
77.8
|
1.0
|
CAU
|
B:J8A501
|
3.0
|
81.5
|
1.0
|
CAN
|
B:J8A501
|
3.4
|
76.9
|
1.0
|
SD
|
B:MET237
|
3.5
|
0.6
|
1.0
|
CD2
|
B:LEU302
|
3.7
|
75.1
|
1.0
|
NBN
|
B:J8A501
|
3.9
|
83.7
|
1.0
|
CAJ
|
B:J8A501
|
4.2
|
79.3
|
1.0
|
CAS
|
B:J8A501
|
4.3
|
85.1
|
1.0
|
CD1
|
B:LEU245
|
4.5
|
91.7
|
1.0
|
CBD
|
B:J8A501
|
4.6
|
78.8
|
1.0
|
CD1
|
B:LEU302
|
4.6
|
72.3
|
1.0
|
CE
|
B:MET237
|
4.7
|
97.8
|
1.0
|
CG
|
B:LEU302
|
4.7
|
79.1
|
1.0
|
CAI
|
B:J8A501
|
4.9
|
82.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 5 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:83.4
occ:1.00
|
FAD
|
B:J8A501
|
0.0
|
83.4
|
1.0
|
CBO
|
B:J8A501
|
1.3
|
77.8
|
1.0
|
FAC
|
B:J8A501
|
2.1
|
84.1
|
1.0
|
FAE
|
B:J8A501
|
2.2
|
80.8
|
1.0
|
CBJ
|
B:J8A501
|
2.2
|
78.4
|
1.0
|
CBG
|
B:J8A501
|
3.0
|
77.8
|
1.0
|
CAU
|
B:J8A501
|
3.1
|
81.5
|
1.0
|
CAN
|
B:J8A501
|
3.2
|
76.9
|
1.0
|
NBN
|
B:J8A501
|
3.3
|
83.7
|
1.0
|
CD2
|
B:HIS309
|
3.6
|
74.9
|
1.0
|
NE2
|
B:HIS309
|
3.8
|
77.8
|
1.0
|
CAS
|
B:J8A501
|
3.9
|
85.1
|
1.0
|
CG2
|
B:ILE327
|
4.0
|
64.2
|
1.0
|
CB
|
B:ASP329
|
4.0
|
78.2
|
1.0
|
C
|
B:SER328
|
4.1
|
69.7
|
1.0
|
CD1
|
B:LEU302
|
4.2
|
72.3
|
1.0
|
O
|
B:SER328
|
4.2
|
71.7
|
1.0
|
CAJ
|
B:J8A501
|
4.3
|
79.3
|
1.0
|
N
|
B:ASP329
|
4.4
|
70.0
|
1.0
|
CA
|
B:SER328
|
4.4
|
69.3
|
1.0
|
CD2
|
B:LEU302
|
4.5
|
75.1
|
1.0
|
CBD
|
B:J8A501
|
4.5
|
78.8
|
1.0
|
O
|
B:ILE327
|
4.6
|
71.6
|
1.0
|
CG
|
B:HIS309
|
4.6
|
75.0
|
1.0
|
N
|
B:SER328
|
4.6
|
66.0
|
1.0
|
CAT
|
B:J8A501
|
4.6
|
79.0
|
1.0
|
C
|
B:ILE327
|
4.7
|
64.7
|
1.0
|
CE1
|
B:HIS309
|
4.8
|
66.5
|
1.0
|
CAI
|
B:J8A501
|
4.9
|
82.6
|
1.0
|
CA
|
B:ASP329
|
4.9
|
73.9
|
1.0
|
CG
|
B:LEU302
|
5.0
|
79.1
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6ega
Go back to
Fluorine Binding Sites List in 6ega
Fluorine binding site 6 out
of 6 in the IRAK4 in Complex with A Type II Inhibitor
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 A Type II Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:80.8
occ:1.00
|
FAE
|
B:J8A501
|
0.0
|
80.8
|
1.0
|
CBO
|
B:J8A501
|
1.3
|
77.8
|
1.0
|
FAD
|
B:J8A501
|
2.2
|
83.4
|
1.0
|
FAC
|
B:J8A501
|
2.2
|
84.1
|
1.0
|
CBJ
|
B:J8A501
|
2.3
|
78.4
|
1.0
|
CAN
|
B:J8A501
|
2.5
|
76.9
|
1.0
|
O
|
B:ILE327
|
3.3
|
71.6
|
1.0
|
CG2
|
B:VAL246
|
3.5
|
72.5
|
1.0
|
CBG
|
B:J8A501
|
3.6
|
77.8
|
1.0
|
CA
|
B:SER328
|
3.7
|
69.3
|
1.0
|
CBD
|
B:J8A501
|
3.9
|
78.8
|
1.0
|
C
|
B:ILE327
|
3.9
|
64.7
|
1.0
|
SD
|
B:MET237
|
4.0
|
0.6
|
1.0
|
OAA
|
B:J8A501
|
4.1
|
75.0
|
1.0
|
C
|
B:SER328
|
4.1
|
69.7
|
1.0
|
N
|
B:SER328
|
4.1
|
66.0
|
1.0
|
CAU
|
B:J8A501
|
4.3
|
81.5
|
1.0
|
N
|
B:ASP329
|
4.3
|
70.0
|
1.0
|
CG2
|
B:ILE327
|
4.5
|
64.2
|
1.0
|
CE
|
B:MET237
|
4.6
|
97.8
|
1.0
|
CAJ
|
B:J8A501
|
4.6
|
79.3
|
1.0
|
N
|
B:VAL246
|
4.7
|
69.6
|
1.0
|
O
|
B:SER328
|
4.7
|
71.7
|
1.0
|
NAY
|
B:J8A501
|
4.7
|
75.6
|
1.0
|
CBB
|
B:J8A501
|
4.8
|
75.7
|
1.0
|
CAI
|
B:J8A501
|
4.8
|
82.6
|
1.0
|
CD2
|
B:LEU245
|
4.8
|
75.4
|
1.0
|
CB
|
B:LEU245
|
4.9
|
73.3
|
1.0
|
CB
|
B:SER328
|
4.9
|
68.9
|
1.0
|
CB
|
B:ILE327
|
4.9
|
68.4
|
1.0
|
CB
|
B:VAL246
|
4.9
|
70.9
|
1.0
|
CB
|
B:ASP329
|
5.0
|
78.2
|
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 19:33:53 2024
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