Fluorine in PDB 8tvm: IRAK4 in Complex with Compound 24

All present enzymatic activity of IRAK4 in Complex with Compound 24:
2.7.11.1;

The structure of IRAK4 in Complex with Compound 24, PDB code: 8tvm 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)	48.52 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.38, 141.98, 87.78, 90, 126.37, 90
R / Rfree (%)	22.1 / 24.7

The binding sites of Fluorine atom in the IRAK4 in Complex with Compound 24 (pdb code 8tvm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the IRAK4 in Complex with Compound 24, PDB code: 8tvm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the IRAK4 in Complex with Compound 24


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 24 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:59.5 occ:1.00 F1 A:VDC501 0.0 59.5 1.0 C8 A:VDC501 1.4 54.4 1.0 C7 A:VDC501 2.4 50.4 1.0 C6 A:VDC501 2.4 52.0 1.0 CD1 A:TYR262 2.7 50.1 1.0 N2 A:VDC501 2.8 40.8 1.0 CE1 A:TYR262 2.8 56.3 1.0 C5 A:VDC501 3.1 41.0 1.0 CB A:LYS213 3.6 55.6 1.0 C9 A:VDC501 3.7 42.2 1.0 CG A:TYR262 3.7 47.0 1.0 CZ A:TYR262 3.8 54.5 1.0 O2 A:VDC501 4.1 43.4 1.0 C4 A:VDC501 4.1 40.2 1.0 CD A:LYS213 4.2 60.6 1.0 CB A:TYR262 4.4 41.2 1.0 CD2 A:TYR262 4.5 47.6 1.0 CG A:LYS213 4.5 56.5 1.0 OH A:TYR262 4.5 70.2 1.0 CE2 A:TYR262 4.5 51.2 1.0 N A:LYS213 4.5 46.4 1.0 C2 A:VDC501 4.6 41.8 1.0 CG1 A:VAL200 4.6 50.4 1.0 CA A:LYS213 4.6 49.7 1.0 CG2 A:VAL200 4.7 48.8 1.0 CB A:ALA211 4.7 39.0 1.0 C3 A:VDC501 4.8 46.4 1.0 O A:LEU260 4.9 43.0 1.0 O A:ALA211 4.9 43.4 1.0

Fluorine binding site 2 out of 4 in the IRAK4 in Complex with Compound 24


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 24 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:59.5 occ:1.00 F1 B:VDC501 0.0 59.5 1.0 C8 B:VDC501 1.4 54.4 1.0 C7 B:VDC501 2.4 50.4 1.0 C6 B:VDC501 2.4 52.0 1.0 N2 B:VDC501 2.8 40.8 1.0 CD1 B:TYR262 3.0 49.6 1.0 C5 B:VDC501 3.1 41.0 1.0 CE1 B:TYR262 3.4 52.8 1.0 CB B:LYS213 3.6 45.0 1.0 C9 B:VDC501 3.7 42.2 1.0 CG B:TYR262 3.9 45.8 1.0 O2 B:VDC501 4.1 43.4 1.0 C4 B:VDC501 4.1 40.2 1.0 CD B:LYS213 4.2 62.8 1.0 CB B:TYR262 4.4 43.9 1.0 CG1 B:VAL200 4.4 43.7 1.0 O B:ALA211 4.4 45.2 1.0 N B:LYS213 4.4 47.7 1.0 CZ B:TYR262 4.4 59.1 1.0 CG B:LYS213 4.5 59.9 1.0 CA B:LYS213 4.5 52.0 1.0 C2 B:VDC501 4.6 41.8 1.0 O B:LEU260 4.7 43.5 1.0 CB B:ALA211 4.7 35.4 1.0 C3 B:VDC501 4.8 46.4 1.0 CG2 B:VAL200 4.8 48.3 1.0 CD2 B:TYR262 4.8 48.9 1.0 C B:ALA211 4.9 49.3 1.0

Fluorine binding site 3 out of 4 in the IRAK4 in Complex with Compound 24


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 24 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:65.7 occ:1.00 F1 C:VDC501 0.0 65.7 1.0 C8 C:VDC501 1.4 59.6 1.0 C7 C:VDC501 2.4 58.2 1.0 C6 C:VDC501 2.4 53.7 1.0 N2 C:VDC501 2.8 57.8 1.0 CE2 C:TYR262 2.9 62.3 1.0 CD2 C:TYR262 3.1 58.7 1.0 C5 C:VDC501 3.2 50.9 1.0 C9 C:VDC501 3.6 53.6 1.0 CB C:LYS213 3.7 65.1 1.0 CZ C:TYR262 3.9 66.6 1.0 O2 C:VDC501 4.0 57.4 1.0 CG C:TYR262 4.0 56.4 1.0 C4 C:VDC501 4.2 53.0 1.0 CG1 C:VAL200 4.2 62.4 1.0 OH C:TYR262 4.5 84.1 1.0 C2 C:VDC501 4.6 53.9 1.0 CE1 C:TYR262 4.7 62.0 1.0 CD1 C:TYR262 4.7 55.8 1.0 C3 C:VDC501 4.8 48.2 1.0 CA C:LYS213 4.8 63.8 1.0 CG2 C:VAL200 4.8 72.9 1.0 N C:LYS213 4.8 54.3 1.0 CB C:TYR262 4.9 49.4 1.0

Fluorine binding site 4 out of 4 in the IRAK4 in Complex with Compound 24


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 24 within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:67.4 occ:1.00 F1 D:VDC501 0.0 67.4 1.0 C8 D:VDC501 1.4 55.4 1.0 C6 D:VDC501 2.4 51.7 1.0 C7 D:VDC501 2.4 55.7 1.0 N2 D:VDC501 2.8 57.1 1.0 CD2 D:TYR262 3.0 52.0 1.0 C5 D:VDC501 3.1 48.8 1.0 CE2 D:TYR262 3.1 59.1 1.0 CE D:LYS213 3.7 70.5 1.0 C9 D:VDC501 3.8 46.7 1.0 CB D:LYS213 3.9 58.0 1.0 CG D:TYR262 4.0 53.6 1.0 CZ D:TYR262 4.0 58.6 1.0 C4 D:VDC501 4.1 52.7 1.0 O2 D:VDC501 4.3 52.1 1.0 CG D:LYS213 4.3 66.8 1.0 NZ D:LYS213 4.3 73.4 1.0 CG2 D:VAL200 4.4 60.4 1.0 CD D:LYS213 4.6 69.1 1.0 OD1 D:ASP329 4.6 63.7 1.0 OH D:TYR262 4.7 77.4 1.0 CB D:TYR262 4.7 48.6 1.0 CD1 D:TYR262 4.7 56.5 1.0 C2 D:VDC501 4.7 49.4 1.0 CE1 D:TYR262 4.7 62.6 1.0 CG1 D:VAL200 4.8 54.8 1.0 C3 D:VDC501 4.8 50.5 1.0

P.N.Bolduc, M.Pfaffenbach, R.Evans, Z.Xin, K.L.Henry, F.Gao, T.Fang, J.Silbereis, J.Vera Rebollar, P.Li, J.V.Chodaparambil, C.Metrick, E.A.Peterson. A Tiny Pocket Packs A Punch: Leveraging Pyridones For the Discovery of Cns-Penetrant Aza-Indazole IRAK4 Inhibitors. Acs Med.Chem.Lett. V. 15 714 2024.
ISSN: ISSN 1948-5875
PubMed: 38746903
DOI: 10.1021/ACSMEDCHEMLETT.4C00102