Fluorine in PDB 7r26: PI3K Delta in Complex with SD5

All present enzymatic activity of PI3K Delta in Complex with SD5:
2.7.1.137; 2.7.1.153;

The structure of PI3K Delta in Complex with SD5, PDB code: 7r26 was solved by S.Gutmann, G.Rummel, B.Shrestha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.13 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.003, 64.53, 117.347, 90, 103.32, 90
R / Rfree (%)	21.5 / 24.1

The binding sites of Fluorine atom in the PI3K Delta in Complex with SD5 (pdb code 7r26). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the PI3K Delta in Complex with SD5, PDB code: 7r26:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the PI3K Delta in Complex with SD5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PI3K Delta in Complex with SD5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:43.2 occ:1.00 F27 A:SD51101 0.0 43.2 1.0 C26 A:SD51101 1.3 42.8 1.0 F29 A:SD51101 2.1 44.0 1.0 F28 A:SD51101 2.1 42.8 1.0 C04 A:SD51101 2.4 40.4 1.0 C09 A:SD51101 2.9 38.0 1.0 C05 A:SD51101 3.3 38.6 1.0 C03 A:SD51101 3.3 39.6 1.0 O A:HOH1248 3.3 35.3 1.0 O A:HOH1239 3.3 43.6 1.0 C08 A:SD51101 3.4 37.7 1.0 C25 A:SD51101 3.7 42.2 1.0 C10 A:SD51101 4.0 38.9 1.0 CG A:PRO758 4.2 37.9 1.0 N20 A:SD51101 4.3 41.3 1.0 CE A:MET752 4.3 53.1 1.0 C06 A:SD51101 4.5 38.2 1.0 C02 A:SD51101 4.6 39.0 1.0 OG A:SER754 4.6 51.6 1.0 OD2 A:ASP911 4.6 46.4 1.0 SD A:MET752 4.6 61.1 1.0 N13 A:SD51101 4.7 37.0 1.0 CB A:PRO758 4.8 37.4 1.0 C24 A:SD51101 5.0 43.5 1.0

Fluorine binding site 2 out of 3 in the PI3K Delta in Complex with SD5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PI3K Delta in Complex with SD5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:42.8 occ:1.00 F28 A:SD51101 0.0 42.8 1.0 C26 A:SD51101 1.3 42.8 1.0 F27 A:SD51101 2.1 43.2 1.0 F29 A:SD51101 2.1 44.0 1.0 C04 A:SD51101 2.4 40.4 1.0 C03 A:SD51101 2.7 39.6 1.0 CD A:LYS779 3.2 47.1 1.0 CG A:PRO758 3.5 37.9 1.0 CE A:LYS779 3.6 51.6 1.0 C05 A:SD51101 3.7 38.6 1.0 CB A:PRO758 3.9 37.4 1.0 NZ A:LYS779 4.0 53.4 1.0 C02 A:SD51101 4.0 39.0 1.0 CG A:LYS779 4.3 41.7 1.0 CD1 A:ILE825 4.3 35.5 1.0 C08 A:SD51101 4.4 37.7 1.0 C09 A:SD51101 4.5 38.0 1.0 CB A:LYS779 4.5 37.1 1.0 CG2 A:ILE777 4.6 31.5 1.0 C06 A:SD51101 4.7 38.2 1.0 O A:HOH1239 4.7 43.6 1.0 O A:HOH1268 4.8 55.2 1.0 CE A:MET752 4.8 53.1 1.0 CD A:PRO758 4.8 37.6 1.0 N01 A:SD51101 4.9 39.1 1.0 O A:HOH1211 4.9 52.1 1.0 N07 A:SD51101 4.9 38.4 1.0 O A:HOH1248 4.9 35.3 1.0

Fluorine binding site 3 out of 3 in the PI3K Delta in Complex with SD5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PI3K Delta in Complex with SD5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:44.0 occ:1.00 F29 A:SD51101 0.0 44.0 1.0 C26 A:SD51101 1.3 42.8 1.0 F27 A:SD51101 2.1 43.2 1.0 F28 A:SD51101 2.1 42.8 1.0 C04 A:SD51101 2.4 40.4 1.0 C05 A:SD51101 2.9 38.6 1.0 C08 A:SD51101 2.9 37.7 1.0 C09 A:SD51101 3.0 38.0 1.0 CE A:MET752 3.4 53.1 1.0 C03 A:SD51101 3.5 39.6 1.0 CG2 A:ILE777 3.6 31.5 1.0 N13 A:SD51101 3.7 37.0 1.0 CD1 A:ILE777 3.8 32.0 1.0 C10 A:SD51101 3.9 38.9 1.0 CD1 A:ILE825 4.1 35.5 1.0 C06 A:SD51101 4.2 38.2 1.0 CB A:PRO758 4.3 37.4 1.0 CG A:PRO758 4.3 37.9 1.0 SD A:MET752 4.3 61.1 1.0 C12 A:SD51101 4.4 36.4 1.0 N11 A:SD51101 4.5 37.7 1.0 N20 A:SD51101 4.5 41.3 1.0 CB A:ILE777 4.6 31.8 1.0 C25 A:SD51101 4.6 42.2 1.0 CG1 A:ILE777 4.6 32.1 1.0 C02 A:SD51101 4.7 39.0 1.0 O A:HOH1239 4.8 43.6 1.0 O A:HOH1248 4.8 35.3 1.0 N07 A:SD51101 4.9 38.4 1.0

R.A.Fairhurst, P.Furet, P.Imbach-Weese, F.Stauffer, H.Rueeger, C.Mccarthy, S.Ripoche, S.Oswald, B.Arnaud, A.Jary, M.Maira, C.Schnell, D.A.Guthy, M.Wartmann, M.Kiffe, S.Desrayaud, F.Blasco, T.Widmer, F.Seiler, S.Gutmann, M.Knapp, G.Caravatti. Identification of Nvp-CLR457 As An Orally Bioavailable Non-Cns-Penetrant Pan-Class Ia Phosphoinositol-3-Kinase Inhibitor. J.Med.Chem. V. 65 8345 2022.
ISSN: ISSN 0022-2623
PubMed: 35500094
DOI: 10.1021/ACS.JMEDCHEM.2C00267