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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:

Cobalt (Co) 6 atoms

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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