Fluorine in PDB 9cj1: Dual Phosphorylated Human P38 Alpha Bound to Nilotinib

All present enzymatic activity of Dual Phosphorylated Human P38 Alpha Bound to Nilotinib:
2.7.11.24;

The structure of Dual Phosphorylated Human P38 Alpha Bound to Nilotinib, PDB code: 9cj1 was solved by E.J.Stadnicki, H.Ludewig, R.Prem Kumar, D.Kern, N.Bradshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.74 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.137, 67.195, 63.016, 90, 97.8, 90
R / Rfree (%)	18.6 / 23.2

The binding sites of Fluorine atom in the Dual Phosphorylated Human P38 Alpha Bound to Nilotinib (pdb code 9cj1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dual Phosphorylated Human P38 Alpha Bound to Nilotinib, PDB code: 9cj1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Dual Phosphorylated Human P38 Alpha Bound to Nilotinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dual Phosphorylated Human P38 Alpha Bound to Nilotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:52.9 occ:1.00 F4 A:NIL402 0.0 52.9 1.0 C2 A:NIL402 1.4 47.7 1.0 F3 A:NIL402 2.2 50.3 1.0 F1 A:NIL402 2.2 41.3 1.0 C5 A:NIL402 2.4 36.6 1.0 C12 A:NIL402 2.9 30.0 1.0 C6 A:NIL402 3.4 39.6 1.0 CG1 A:VAL83 3.9 34.0 1.0 C11 A:NIL402 4.2 34.6 1.0 CD1 A:ILE141 4.3 38.1 1.0 SD A:MET78 4.5 42.9 1.0 O A:ILE166 4.6 34.3 1.0 C8 A:NIL402 4.6 43.9 1.0 CG2 A:ILE84 4.6 40.2 1.0 CD2 A:LEU75 4.8 34.5 1.0 CG1 A:ILE141 4.8 30.3 1.0 C9 A:NIL402 4.9 36.0 1.0 CG A:MET78 4.9 41.3 1.0 O17 A:NIL402 5.0 33.1 1.0 CD2 A:LEU74 5.0 51.5 1.0 CA A:LEU167 5.0 33.1 1.0

Fluorine binding site 2 out of 3 in the Dual Phosphorylated Human P38 Alpha Bound to Nilotinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dual Phosphorylated Human P38 Alpha Bound to Nilotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:50.3 occ:1.00 F3 A:NIL402 0.0 50.3 1.0 C2 A:NIL402 1.4 47.7 1.0 F1 A:NIL402 2.2 41.3 1.0 F4 A:NIL402 2.2 52.9 1.0 C5 A:NIL402 2.4 36.6 1.0 C6 A:NIL402 2.8 39.6 1.0 C12 A:NIL402 3.7 30.0 1.0 CD2 A:HIS148 3.8 28.9 1.0 O A:HOH510 4.1 51.8 1.0 CD1 A:ILE141 4.1 38.1 1.0 C8 A:NIL402 4.2 43.9 1.0 O A:HOH587 4.3 51.9 1.0 NE2 A:HIS148 4.4 27.3 1.0 CG A:HIS148 4.5 24.1 1.0 CD2 A:LEU74 4.5 51.5 1.0 CG2 A:ILE146 4.7 39.0 1.0 CG1 A:ILE141 4.7 30.3 1.0 CG2 A:ILE141 4.7 34.8 1.0 C11 A:NIL402 4.8 34.6 1.0 CB A:HIS148 4.8 25.6 1.0 CA A:HIS148 4.9 25.8 1.0 CB A:ASP168 4.9 31.1 1.0 C9 A:NIL402 5.0 36.0 1.0

Fluorine binding site 3 out of 3 in the Dual Phosphorylated Human P38 Alpha Bound to Nilotinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dual Phosphorylated Human P38 Alpha Bound to Nilotinib within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:41.3 occ:1.00 F1 A:NIL402 0.0 41.3 1.0 C2 A:NIL402 1.4 47.7 1.0 F3 A:NIL402 2.2 50.3 1.0 F4 A:NIL402 2.2 52.9 1.0 C5 A:NIL402 2.4 36.6 1.0 C12 A:NIL402 2.9 30.0 1.0 C A:LEU167 3.3 30.9 1.0 CD2 A:HIS148 3.4 28.9 1.0 NE2 A:HIS148 3.5 27.3 1.0 C6 A:NIL402 3.5 39.6 1.0 O A:LEU167 3.6 31.6 1.0 N A:ASP168 3.6 32.6 1.0 CA A:LEU167 3.6 33.1 1.0 CB A:ASP168 3.8 31.1 1.0 CG2 A:ILE166 3.9 27.8 1.0 N A:LEU167 4.1 29.8 1.0 O A:ILE166 4.2 34.3 1.0 C11 A:NIL402 4.2 34.6 1.0 C A:ILE166 4.3 31.8 1.0 CA A:ASP168 4.3 37.4 1.0 O17 A:NIL402 4.5 33.1 1.0 CG A:HIS148 4.5 24.1 1.0 CE1 A:HIS148 4.6 31.4 1.0 C8 A:NIL402 4.6 43.9 1.0 CD1 A:ILE141 4.7 38.1 1.0 CB A:ILE166 4.9 30.4 1.0 C9 A:NIL402 4.9 36.0 1.0 O A:HOH510 4.9 51.8 1.0 CG A:ASP168 5.0 43.3 1.0

E.J.Stadnicki, H.Ludewig, R.P.Kumar, X.Wang, Y.Qiao, D.Kern, N.Bradshaw. Dual-Action Kinase Inhibitors Influence P38 Alpha Map Kinase Dephosphorylation. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39149408
DOI: 10.1101/2024.05.15.594272