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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:

Cobalt (Co) 4 atoms

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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