Fluorine in PDB 2xnp: Structure of NEK2 Bound to CCT244858

All present enzymatic activity of Structure of NEK2 Bound to CCT244858:
2.7.11.1;

The structure of Structure of NEK2 Bound to CCT244858, PDB code: 2xnp was solved by C.Mas-Droux, R.Bayliss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.784 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.640, 56.880, 81.840, 90.00, 133.63, 90.00
R / Rfree (%)	15.66 / 20.12

The structure of Structure of NEK2 Bound to CCT244858 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Structure of NEK2 Bound to CCT244858 (pdb code 2xnp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of NEK2 Bound to CCT244858, PDB code: 2xnp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of NEK2 Bound to CCT244858


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of NEK2 Bound to CCT244858 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:26.2 occ:1.00 F39 A:WCX1280 0.0 26.2 1.0 C36 A:WCX1280 1.3 24.8 1.0 F38 A:WCX1280 2.2 24.1 1.0 F37 A:WCX1280 2.2 26.0 1.0 C35 A:WCX1280 2.4 19.9 1.0 C34 A:WCX1280 2.7 24.1 1.0 CG2 A:ILE14 3.4 21.5 0.2 O A:ILE14 3.4 28.4 1.0 CA A:GLY15 3.5 24.3 1.0 C A:ILE14 3.6 26.2 1.0 N A:GLY15 3.7 21.5 1.0 C30 A:WCX1280 3.8 20.8 1.0 CB A:ILE14 4.1 22.1 0.2 CG1 A:ILE14 4.1 24.5 0.8 C21 A:WCX1280 4.1 22.1 1.0 C33 A:WCX1280 4.2 25.1 1.0 C22 A:WCX1280 4.2 17.1 1.0 O A:HOH2036 4.3 47.6 1.0 CB A:ILE14 4.3 22.8 0.8 O A:HOH2020 4.4 46.9 1.0 C02 A:WCX1280 4.4 29.4 1.0 CB A:CYS22 4.6 18.7 0.7 CA A:ILE14 4.6 21.8 0.2 O A:HOH2013 4.6 53.3 1.0 CA A:ILE14 4.6 22.1 0.8 C A:GLY15 4.7 31.6 1.0 CB A:CYS22 4.8 17.7 0.3 SG A:CYS22 4.8 19.6 0.7 CD1 A:ILE14 4.9 25.7 0.8 OH A:TYR19 4.9 49.2 1.0 C01 A:WCX1280 4.9 29.4 1.0 C31 A:WCX1280 4.9 18.9 1.0

Fluorine binding site 2 out of 3 in the Structure of NEK2 Bound to CCT244858


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of NEK2 Bound to CCT244858 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:24.1 occ:1.00 F38 A:WCX1280 0.0 24.1 1.0 C36 A:WCX1280 1.4 24.8 1.0 F39 A:WCX1280 2.2 26.2 1.0 F37 A:WCX1280 2.2 26.0 1.0 C35 A:WCX1280 2.4 19.9 1.0 SG A:CYS22 3.0 19.6 0.7 C30 A:WCX1280 3.1 20.8 1.0 C02 A:WCX1280 3.1 29.4 1.0 C22 A:WCX1280 3.3 17.1 1.0 CB A:CYS22 3.4 18.7 0.7 C05 A:WCX1280 3.4 14.7 1.0 C34 A:WCX1280 3.4 24.1 1.0 CB A:CYS22 3.5 17.7 0.3 CG1 A:ILE14 3.6 24.5 0.8 CG2 A:ILE14 3.8 21.5 0.2 C21 A:WCX1280 3.9 22.1 1.0 CD1 A:ILE14 3.9 25.7 0.8 C23 A:WCX1280 3.9 12.8 1.0 SG A:CYS22 4.1 18.0 0.3 C01 A:WCX1280 4.1 29.4 1.0 CB A:ILE14 4.2 22.1 0.2 O03 A:WCX1280 4.2 23.5 1.0 C04 A:WCX1280 4.3 22.1 1.0 N07 A:WCX1280 4.4 15.6 1.0 C06 A:WCX1280 4.4 18.4 1.0 C31 A:WCX1280 4.5 18.9 1.0 CB A:ILE14 4.6 22.8 0.8 N A:GLY15 4.7 21.5 1.0 C33 A:WCX1280 4.7 25.1 1.0 C A:ILE14 4.8 26.2 1.0 C12 A:WCX1280 4.8 15.0 1.0 C10 A:WCX1280 4.8 13.2 1.0 CA A:GLY15 4.8 24.3 1.0 CA A:CYS22 4.9 17.0 0.7 CA A:CYS22 4.9 17.5 0.3 O A:ILE14 5.0 28.4 1.0

Fluorine binding site 3 out of 3 in the Structure of NEK2 Bound to CCT244858


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of NEK2 Bound to CCT244858 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1280 b:26.0 occ:1.00 F37 A:WCX1280 0.0 26.0 1.0 C36 A:WCX1280 1.4 24.8 1.0 F39 A:WCX1280 2.2 26.2 1.0 F38 A:WCX1280 2.2 24.1 1.0 C35 A:WCX1280 2.4 19.9 1.0 OH A:TYR19 3.0 49.2 1.0 C02 A:WCX1280 3.0 29.4 1.0 C01 A:WCX1280 3.1 29.4 1.0 C30 A:WCX1280 3.1 20.8 1.0 CB A:CYS22 3.3 18.7 0.7 O A:HOH2020 3.3 46.9 1.0 CB A:CYS22 3.4 17.7 0.3 C34 A:WCX1280 3.5 24.1 1.0 SG A:CYS22 3.6 18.0 0.3 CA A:GLY15 3.6 24.3 1.0 SG A:CYS22 3.9 19.6 0.7 N A:GLY15 4.1 21.5 1.0 CZ A:TYR19 4.1 57.4 1.0 C A:GLY15 4.2 31.6 1.0 O03 A:WCX1280 4.4 23.5 1.0 C31 A:WCX1280 4.5 18.9 1.0 O A:GLY15 4.5 28.1 1.0 CA A:CYS22 4.6 17.0 0.7 CA A:CYS22 4.7 17.5 0.3 C A:ILE14 4.7 26.2 1.0 N A:CYS22 4.7 21.5 1.0 CE2 A:TYR19 4.8 61.5 1.0 C33 A:WCX1280 4.8 25.1 1.0 CG1 A:ILE14 4.8 24.5 0.8 C05 A:WCX1280 4.9 14.7 1.0 O A:ILE14 4.9 28.4 1.0 N A:THR16 4.9 25.8 1.0

S.Solanki, P.Innocenti, C.Mas-Droux, K.Boxall, C.Barillari, R.L.Van Montfort, G.W.Aherne, R.Bayliss, S.Hoelder. Benzimidazole Inhibitors Induce A Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (NEK2) Without Binding to the Back Pocket and Reveal A Nonlinear Structure-Activity Relationship. J.Med.Chem. V. 54 1626 2011.
ISSN: ISSN 0022-2623
PubMed: 21366329
DOI: 10.1021/JM1011726