Fluorine in PDB 4afe: NEK2 Bound to Hybrid Compound 21

All present enzymatic activity of NEK2 Bound to Hybrid Compound 21:
2.7.11.1;

The structure of NEK2 Bound to Hybrid Compound 21, PDB code: 4afe was solved by S.Yeoh, P.Innocenti, S.Hoelder, R.Bayliss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.286 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.039, 56.724, 74.279, 90.00, 127.10, 90.00
R / Rfree (%)	21.65 / 24.82

The binding sites of Fluorine atom in the NEK2 Bound to Hybrid Compound 21 (pdb code 4afe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the NEK2 Bound to Hybrid Compound 21, PDB code: 4afe:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the NEK2 Bound to Hybrid Compound 21


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of NEK2 Bound to Hybrid Compound 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:52.5 occ:1.00 F06 A:GGY1280 0.0 52.5 1.0 C05 A:GGY1280 1.3 55.6 1.0 F08 A:GGY1280 2.2 59.5 1.0 F07 A:GGY1280 2.2 48.8 1.0 C04 A:GGY1280 2.3 46.8 1.0 C03 A:GGY1280 3.6 47.5 1.0 O A:HOH2001 3.9 52.6 1.0 C02 A:GGY1280 4.2 46.9 1.0 CA A:GLY15 4.2 39.8 1.0 S24 A:GGY1280 4.5 45.2 1.0 O A:HOH2010 4.5 30.9 1.0 C01 A:GGY1280 4.6 50.1 1.0 OH A:TYR19 4.6 57.1 1.0 CG2 A:ILE14 4.7 43.0 1.0 N A:GLY15 4.7 36.8 1.0 O A:ILE14 4.8 40.4 1.0 C A:ILE14 5.0 36.0 1.0

Fluorine binding site 2 out of 3 in the NEK2 Bound to Hybrid Compound 21


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of NEK2 Bound to Hybrid Compound 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:48.8 occ:1.00 F07 A:GGY1280 0.0 48.8 1.0 C05 A:GGY1280 1.3 55.6 1.0 F08 A:GGY1280 2.2 59.5 1.0 F06 A:GGY1280 2.2 52.5 1.0 C04 A:GGY1280 2.3 46.8 1.0 C02 A:GGY1280 2.9 46.9 1.0 C03 A:GGY1280 2.9 47.5 1.0 C11 A:GGY1280 3.5 35.3 1.0 C01 A:GGY1280 3.7 50.1 1.0 SG A:CYS22 3.8 48.9 1.0 C14 A:GGY1280 3.8 29.1 1.0 O09 A:GGY1280 3.9 41.4 1.0 S24 A:GGY1280 4.0 45.2 1.0 C10 A:GGY1280 4.1 35.2 1.0 CB A:CYS22 4.3 37.5 1.0 CG2 A:ILE14 4.3 43.0 1.0 C12 A:GGY1280 4.4 37.0 1.0 C13 A:GGY1280 4.5 26.6 1.0 C15 A:GGY1280 4.7 25.1 1.0 C16 A:GGY1280 4.7 29.1 1.0 CB A:ILE14 4.8 36.5 1.0 N A:GLY15 4.9 36.8 1.0 CA A:GLY15 4.9 39.8 1.0

Fluorine binding site 3 out of 3 in the NEK2 Bound to Hybrid Compound 21


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of NEK2 Bound to Hybrid Compound 21 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:59.5 occ:1.00 F08 A:GGY1280 0.0 59.5 1.0 C05 A:GGY1280 1.3 55.6 1.0 F06 A:GGY1280 2.2 52.5 1.0 F07 A:GGY1280 2.2 48.8 1.0 C04 A:GGY1280 2.3 46.8 1.0 C01 A:GGY1280 2.7 50.1 1.0 C02 A:GGY1280 2.8 46.9 1.0 C03 A:GGY1280 2.9 47.5 1.0 OH A:TYR19 2.9 57.1 1.0 O A:HOH2001 3.4 52.6 1.0 CB A:CYS22 3.7 37.5 1.0 CA A:GLY15 3.8 39.8 1.0 CZ A:TYR19 3.8 60.1 1.0 SG A:CYS22 4.1 48.9 1.0 O09 A:GGY1280 4.2 41.4 1.0 C A:GLY15 4.3 42.1 1.0 N A:GLY15 4.3 36.8 1.0 CE1 A:TYR19 4.4 66.1 1.0 CE2 A:TYR19 4.5 51.4 1.0 O A:GLY15 4.7 45.3 1.0 N A:THR16 4.8 48.9 1.0 C11 A:GGY1280 4.9 35.3 1.0

P.Innocenti, K.M.Cheung, S.Solanki, C.Mas-Droux, F.Rowan, S.Yeoh, K.Boxall, M.Westlake, L.Pickard, T.Hardy, J.E.Baxter, G.W.Aherne, R.Bayliss, A.M.Fry, S.Hoelder. Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase NEK2: Structure-Activity Relationship, Structural Biology, and Cellular Activity. J.Med.Chem. V. 55 3228 2012.
ISSN: ISSN 0022-2623
PubMed: 22404346
DOI: 10.1021/JM201683B