Fluorine in PDB 8ucb: IRAK4 in Complex with Compound 8

Enzymatic activity of IRAK4 in Complex with Compound 8

All present enzymatic activity of IRAK4 in Complex with Compound 8:
2.7.11.1;

Protein crystallography data

The structure of IRAK4 in Complex with Compound 8, PDB code: 8ucb was solved by C.M.Metrick, J.V.Chodaparambil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.31 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.62, 140.85, 87.53, 90, 125.7, 90
R / Rfree (%) 20.7 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the IRAK4 in Complex with Compound 8 (pdb code 8ucb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the IRAK4 in Complex with Compound 8, PDB code: 8ucb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 1 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:44.0
occ:1.00
 F1 A:X1T501 0.0 44.0 1.0
C17 A:X1T501 1.3 38.8 1.0
F2 A:X1T501 2.1 48.9 1.0
C16 A:X1T501 2.3 33.5 1.0
N4 A:X1T501 3.1 29.2 1.0
C15 A:X1T501 3.2 34.6 1.0
CG2 A:VAL200 3.3 36.3 1.0
O A:HOH688 3.7 46.4 1.0
CE1 A:TYR262 3.7 42.9 1.0
CB A:LYS213 3.8 35.1 1.0
CG1 A:VAL200 3.9 38.1 1.0
CD A:LYS213 3.9 44.1 1.0
CD1 A:TYR262 4.0 33.5 1.0
CB A:VAL200 4.2 38.1 1.0
CG A:LYS213 4.2 41.6 1.0
C12 A:X1T501 4.3 30.4 1.0
CZ A:TYR262 4.4 40.2 1.0
C14 A:X1T501 4.4 30.0 1.0
CE A:LYS213 4.5 51.7 1.0
O A:HOH652 4.6 43.3 1.0
OH A:TYR262 4.8 48.0 1.0
C13 A:X1T501 4.9 31.0 1.0
CA A:LYS213 4.9 36.2 1.0
CG A:TYR262 4.9 32.4 1.0

Fluorine binding site 2 out of 8 in 8ucb

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Fluorine binding site 2 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:48.9
occ:1.00
 F2 A:X1T501 0.0 48.9 1.0
C17 A:X1T501 1.3 38.8 1.0
F1 A:X1T501 2.1 44.0 1.0
C16 A:X1T501 2.3 33.5 1.0
C15 A:X1T501 2.8 34.6 1.0
O A:HOH688 3.1 46.4 1.0
O A:HOH652 3.3 43.3 1.0
N4 A:X1T501 3.5 29.2 1.0
CB A:SER328 3.6 29.2 1.0
OG A:SER328 3.6 40.3 1.0
C14 A:X1T501 4.2 30.0 1.0
CE1 A:TYR262 4.2 42.9 1.0
CZ A:TYR262 4.3 40.2 1.0
CD1 A:LEU318 4.3 37.5 1.0
O A:HOH667 4.4 41.8 1.0
OH A:TYR262 4.4 48.0 1.0
N A:ASP329 4.4 33.8 1.0
C12 A:X1T501 4.6 30.4 1.0
CD1 A:TYR262 4.7 33.5 1.0
CE2 A:TYR262 4.8 37.2 1.0
CD A:LYS213 4.8 44.1 1.0
CA A:SER328 4.9 32.3 1.0
C13 A:X1T501 4.9 31.0 1.0
CG2 A:VAL200 4.9 36.3 1.0

Fluorine binding site 3 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 3 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:44.0
occ:1.00
 F1 B:X1T501 0.0 44.0 1.0
C17 B:X1T501 1.3 38.8 1.0
F2 B:X1T501 2.1 48.9 1.0
C16 B:X1T501 2.3 33.5 1.0
N4 B:X1T501 3.1 29.2 1.0
C15 B:X1T501 3.2 34.6 1.0
CG2 B:VAL200 3.3 29.2 1.0
CE1 B:TYR262 3.7 28.7 1.0
CG1 B:VAL200 3.8 29.2 1.0
O B:HOH695 3.8 51.9 1.0
CB B:LYS213 3.9 26.7 1.0
CD1 B:TYR262 4.0 26.3 1.0
CD B:LYS213 4.1 33.4 1.0
CB B:VAL200 4.2 31.0 1.0
O B:HOH624 4.2 39.1 1.0
C12 B:X1T501 4.3 30.4 1.0
CG B:LYS213 4.4 28.4 1.0
C14 B:X1T501 4.4 30.0 1.0
CZ B:TYR262 4.4 32.6 1.0
O B:HOH628 4.7 42.6 1.0
CE B:LYS213 4.7 48.5 1.0
OH B:TYR262 4.8 36.5 1.0
C13 B:X1T501 4.9 31.0 1.0
CA B:LYS213 4.9 27.3 1.0
CG B:TYR262 4.9 28.2 1.0

Fluorine binding site 4 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 4 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:48.9
occ:1.00
 F2 B:X1T501 0.0 48.9 1.0
C17 B:X1T501 1.3 38.8 1.0
F1 B:X1T501 2.1 44.0 1.0
C16 B:X1T501 2.3 33.5 1.0
C15 B:X1T501 2.8 34.6 1.0
O B:HOH628 3.2 42.6 1.0
O B:HOH695 3.3 51.9 1.0
O B:HOH624 3.4 39.1 1.0
N4 B:X1T501 3.5 29.2 1.0
O B:HOH643 3.7 40.6 1.0
CB B:SER328 3.8 27.2 1.0
OG B:SER328 3.9 33.7 1.0
C14 B:X1T501 4.2 30.0 1.0
CE1 B:TYR262 4.2 28.7 1.0
CZ B:TYR262 4.2 32.6 1.0
N B:ASP329 4.4 31.6 1.0
OH B:TYR262 4.4 36.5 1.0
CD1 B:LEU318 4.4 24.7 1.0
C12 B:X1T501 4.6 30.4 1.0
CD1 B:TYR262 4.6 26.3 1.0
CE2 B:TYR262 4.7 27.8 1.0
CG2 B:VAL200 4.9 29.2 1.0
C13 B:X1T501 4.9 31.0 1.0
CD B:LYS213 4.9 33.4 1.0
CA B:ASP329 4.9 36.2 1.0
CA B:SER328 5.0 25.9 1.0

Fluorine binding site 5 out of 8 in 8ucb

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Fluorine binding site 5 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:44.0
occ:1.00
 F1 C:X1T501 0.0 44.0 1.0
C17 C:X1T501 1.3 38.8 1.0
F2 C:X1T501 2.1 48.9 1.0
C16 C:X1T501 2.3 33.5 1.0
N4 C:X1T501 3.1 29.2 1.0
C15 C:X1T501 3.2 34.6 1.0
CG2 C:VAL200 3.3 32.5 1.0
CE1 C:TYR262 3.7 34.3 1.0
CB C:LYS213 3.8 28.2 1.0
CD C:LYS213 3.8 37.5 1.0
CG1 C:VAL200 3.9 28.6 1.0
CD1 C:TYR262 4.0 30.8 1.0
CB C:VAL200 4.2 28.8 1.0
O C:HOH634 4.2 40.0 1.0
C12 C:X1T501 4.3 30.4 1.0
CG C:LYS213 4.3 29.3 1.0
CZ C:TYR262 4.4 36.2 1.0
C14 C:X1T501 4.4 30.0 1.0
CA C:LYS213 4.7 25.2 1.0
OH C:TYR262 4.8 37.6 1.0
N C:LYS213 4.8 26.3 1.0
C13 C:X1T501 4.9 31.0 1.0
O C:HOH624 4.9 42.2 1.0
CG C:TYR262 4.9 25.4 1.0

Fluorine binding site 6 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 6 out of 8 in the IRAK4 in Complex with Compound 8


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 Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:48.9
occ:1.00
 F2 C:X1T501 0.0 48.9 1.0
C17 C:X1T501 1.3 38.8 1.0
F1 C:X1T501 2.1 44.0 1.0
C16 C:X1T501 2.3 33.5 1.0
C15 C:X1T501 2.8 34.6 1.0
O C:HOH634 3.4 40.0 1.0
N4 C:X1T501 3.5 29.2 1.0
O C:HOH624 3.5 42.2 1.0
O C:HOH678 3.6 41.2 1.0
CB C:SER328 4.0 25.4 1.0
OG C:SER328 4.0 35.4 1.0
CE1 C:TYR262 4.0 34.3 1.0
CZ C:TYR262 4.1 36.2 1.0
C14 C:X1T501 4.1 30.0 1.0
OH C:TYR262 4.3 37.6 1.0
CD1 C:TYR262 4.5 30.8 1.0
CD C:LYS213 4.5 37.5 1.0
CD1 C:LEU318 4.5 32.9 1.0
N C:ASP329 4.6 31.1 1.0
C12 C:X1T501 4.6 30.4 1.0
CE2 C:TYR262 4.7 28.0 1.0
CG2 C:VAL200 4.9 32.5 1.0
C13 C:X1T501 4.9 31.0 1.0

Fluorine binding site 7 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 7 out of 8 in the IRAK4 in Complex with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of IRAK4 in Complex with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:44.0
occ:1.00
 F1 D:X1T501 0.0 44.0 1.0
C17 D:X1T501 1.3 38.8 1.0
F2 D:X1T501 2.1 48.9 1.0
C16 D:X1T501 2.3 33.5 1.0
N4 D:X1T501 3.1 29.2 1.0
C15 D:X1T501 3.2 34.6 1.0
O D:HOH617 3.4 57.1 1.0
CG2 D:VAL200 3.5 37.0 1.0
CE2 D:TYR262 3.7 39.4 1.0
CD D:LYS213 3.8 35.9 1.0
CB D:LYS213 3.8 32.7 1.0
CG1 D:VAL200 3.8 34.8 1.0
CD2 D:TYR262 3.9 33.3 1.0
O D:HOH641 4.0 40.2 1.0
CG D:LYS213 4.3 34.4 1.0
C12 D:X1T501 4.3 30.4 1.0
CB D:VAL200 4.3 39.5 1.0
C14 D:X1T501 4.4 30.0 1.0
CZ D:TYR262 4.5 41.0 1.0
O D:HOH621 4.7 40.6 1.0
CA D:LYS213 4.8 31.6 1.0
C13 D:X1T501 4.9 31.0 1.0
CG D:TYR262 4.9 31.5 1.0
OH D:TYR262 4.9 41.9 1.0
CE D:LYS213 4.9 49.0 1.0
N D:LYS213 5.0 34.0 1.0

Fluorine binding site 8 out of 8 in 8ucb

Go back to Fluorine Binding Sites List in 8ucb
Fluorine binding site 8 out of 8 in the IRAK4 in Complex with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of IRAK4 in Complex with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:48.9
occ:1.00
 F2 D:X1T501 0.0 48.9 1.0
C17 D:X1T501 1.3 38.8 1.0
F1 D:X1T501 2.1 44.0 1.0
C16 D:X1T501 2.3 33.5 1.0
O D:HOH617 2.6 57.1 1.0
C15 D:X1T501 2.8 34.6 1.0
O D:HOH621 3.2 40.6 1.0
O D:HOH641 3.3 40.2 1.0
N4 D:X1T501 3.5 29.2 1.0
CB D:SER328 3.8 30.5 1.0
OG D:SER328 3.8 40.8 1.0
C14 D:X1T501 4.2 30.0 1.0
CE2 D:TYR262 4.2 39.4 1.0
O D:HOH654 4.3 42.5 1.0
CZ D:TYR262 4.3 41.0 1.0
CD1 D:LEU318 4.4 31.6 1.0
OH D:TYR262 4.5 41.9 1.0
N D:ASP329 4.6 31.0 1.0
C12 D:X1T501 4.6 30.4 1.0
CD2 D:TYR262 4.6 33.3 1.0
CD D:LYS213 4.6 35.9 1.0
CE1 D:TYR262 4.9 34.5 1.0
C13 D:X1T501 4.9 31.0 1.0

Reference:

R.Evans, P.N.Bolduc, M.Pfaffenbach, F.Gao, T.May-Dracka, T.Fang, B.T.Hopkins, J.V.Chodaparambil, K.L.Henry, P.Li, C.Metrick, A.Nelson, P.Trapa, A.Thomas, L.Burkly, E.A.Peterson. The Discovery of 7-Isopropoxy-2-(1-Methyl-2-Oxabicyclo[2.1.1]Hexan-4-Yl)- N -(6-Methylpyrazolo[1,5- A ]Pyrimidin-3-Yl)Imidazo[1,2- A ]Pyrimidine-6-Carboxamide (Bio-7488), A Potent, Selective, and Cns-Penetrant IRAK4 Inhibitor For the Treatment of Ischemic Stroke. J.Med.Chem. V. 67 4676 2024.
ISSN: ISSN 0022-2623
PubMed: 38467640
DOI: 10.1021/ACS.JMEDCHEM.3C02226
Page generated: Sat Aug 3 00:51:09 2024

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