Fluorine in PDB 2fky: Crystal Structure of Ksp in Complex with Inhibitor 13

The structure of Crystal Structure of Ksp in Complex with Inhibitor 13, PDB code: 2fky was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.200, 79.600, 159.000, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.3

The structure of Crystal Structure of Ksp in Complex with Inhibitor 13 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Ksp in Complex with Inhibitor 13 (pdb code 2fky). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Ksp in Complex with Inhibitor 13, PDB code: 2fky:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ksp in Complex with Inhibitor 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:14.9 occ:1.00 F40 A:N2T604 0.0 14.9 1.0 C4 A:N2T604 1.3 17.6 1.0 C3 A:N2T604 2.3 19.5 1.0 C5 A:N2T604 2.4 16.5 1.0 C14 A:N2T604 2.7 22.0 1.0 C10 A:N2T604 2.7 22.0 1.0 CB A:GLU116 3.1 19.6 1.0 CG A:GLU116 3.4 23.4 1.0 CB A:ILE136 3.6 19.2 1.0 CA A:GLU116 3.6 21.5 1.0 C2 A:N2T604 3.6 19.6 1.0 C6 A:N2T604 3.7 18.3 1.0 CG2 A:ILE136 3.8 15.8 1.0 CD1 A:ILE136 3.8 17.9 1.0 CD A:PRO137 3.8 20.4 1.0 CD A:GLU116 3.9 23.2 1.0 C1 A:N2T604 4.1 19.8 1.0 C13 A:N2T604 4.2 22.7 1.0 O A:GLU116 4.2 21.4 1.0 C11 A:N2T604 4.2 24.4 1.0 CG1 A:ILE136 4.3 18.2 1.0 OE1 A:GLU116 4.3 24.6 1.0 OE2 A:GLU116 4.3 25.1 1.0 C A:GLU116 4.3 22.1 1.0 CD1 A:LEU214 4.4 23.7 1.0 CD2 A:LEU214 4.4 21.9 1.0 N A:PRO137 4.6 20.0 1.0 N A:GLU116 4.8 19.5 1.0 O A:MET115 4.8 19.0 1.0 CA A:ILE136 4.8 18.5 1.0 CG A:LEU214 4.8 24.3 1.0 N12 A:N2T604 4.9 25.6 1.0 CG A:PRO137 4.9 22.1 1.0 CB A:LEU214 5.0 23.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ksp in Complex with Inhibitor 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:24.1 occ:1.00 F41 A:N2T604 0.0 24.1 1.0 C1 A:N2T604 1.3 19.8 1.0 C6 A:N2T604 2.3 18.3 1.0 C2 A:N2T604 2.3 19.6 1.0 C A:GLY217 3.3 22.6 1.0 N A:ALA218 3.4 21.5 1.0 CA A:GLY217 3.4 24.7 1.0 NH1 A:ARG221 3.6 24.7 1.0 CD2 A:LEU160 3.6 26.3 1.0 C5 A:N2T604 3.6 16.5 1.0 O A:LEU214 3.6 27.4 1.0 C3 A:N2T604 3.6 19.5 1.0 CZ A:ARG221 3.7 24.3 1.0 O A:GLY217 3.9 21.4 1.0 NE A:ARG221 4.0 24.7 1.0 C4 A:N2T604 4.1 17.6 1.0 NH2 A:ARG221 4.1 23.4 1.0 CA A:ALA218 4.1 22.9 1.0 CD A:ARG221 4.3 24.3 1.0 N A:GLY217 4.3 26.6 1.0 C A:LEU214 4.5 27.5 1.0 CA A:LEU214 4.6 26.3 1.0 CB A:ALA218 4.7 20.9 1.0 C10 A:N2T604 4.9 22.0 1.0 OE2 A:GLU116 4.9 25.1 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Ksp in Complex with Inhibitor 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F605 b:21.3 occ:1.00 F40 B:N2T605 0.0 21.3 1.0 C4 B:N2T605 1.3 19.3 1.0 C3 B:N2T605 2.3 20.4 1.0 C5 B:N2T605 2.3 20.4 1.0 C10 B:N2T605 2.8 19.8 1.0 C14 B:N2T605 2.9 21.6 1.0 CG B:GLU116 3.3 19.0 1.0 CB B:GLU116 3.4 18.2 1.0 CG2 B:ILE136 3.6 14.2 1.0 CB B:ILE136 3.6 18.2 1.0 C2 B:N2T605 3.6 19.4 1.0 C6 B:N2T605 3.6 19.5 1.0 CA B:GLU116 3.8 19.0 1.0 CD B:PRO137 3.8 19.0 1.0 CD1 B:ILE136 4.0 18.1 1.0 CD B:GLU116 4.0 20.2 1.0 C1 B:N2T605 4.0 20.3 1.0 CD2 B:LEU214 4.1 21.1 1.0 CD1 B:LEU214 4.2 20.6 1.0 OE1 B:GLU116 4.2 21.0 1.0 C11 B:N2T605 4.3 22.9 1.0 C13 B:N2T605 4.3 23.2 1.0 O B:GLU116 4.3 17.6 1.0 CG1 B:ILE136 4.4 17.3 1.0 C B:GLU116 4.5 19.8 1.0 CG B:LEU214 4.6 21.9 1.0 N B:PRO137 4.6 18.0 1.0 CG B:PRO137 4.8 17.8 1.0 OE2 B:GLU116 4.8 19.9 1.0 O B:MET115 4.8 17.7 1.0 CA B:ILE136 4.8 17.8 1.0 CB B:LEU214 4.9 20.3 1.0 N B:GLU116 5.0 16.7 1.0 N12 B:N2T605 5.0 24.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Ksp in Complex with Inhibitor 13 within 5.0Å range: probe atom residue distance (Å) B Occ B:F605 b:25.4 occ:1.00 F41 B:N2T605 0.0 25.4 1.0 C1 B:N2T605 1.3 20.3 1.0 C6 B:N2T605 2.3 19.5 1.0 C2 B:N2T605 2.3 19.4 1.0 C B:GLY217 3.2 21.5 1.0 N B:ALA218 3.2 20.0 1.0 CA B:GLY217 3.3 21.3 1.0 NH1 B:ARG221 3.5 21.2 1.0 C3 B:N2T605 3.6 20.4 1.0 CZ B:ARG221 3.6 22.8 1.0 C5 B:N2T605 3.6 20.4 1.0 O B:LEU214 3.7 21.0 1.0 CD2 B:LEU160 3.7 13.1 1.0 O B:GLY217 3.9 20.7 1.0 NE B:ARG221 3.9 22.2 1.0 CA B:ALA218 4.0 21.5 1.0 C4 B:N2T605 4.1 19.3 1.0 NH2 B:ARG221 4.1 18.9 1.0 CD B:ARG221 4.1 21.2 1.0 N B:GLY217 4.3 22.1 1.0 C B:LEU214 4.6 22.5 1.0 CB B:ALA218 4.7 18.8 1.0 CA B:LEU214 4.8 21.5 1.0 C10 B:N2T605 4.8 19.8 1.0 CG B:ARG221 4.9 21.5 1.0 OE1 B:GLU116 5.0 21.0 1.0

M.E.Fraley, R.M.Garbaccio, K.L.Arrington, W.F.Hoffman, E.S.Tasber, P.J.Coleman, C.A.Buser, E.S.Walsh, K.Hamilton, C.Fernandes, M.D.Schaber, R.B.Lobell, W.Tao, V.J.South, Y.Yan, L.C.Kuo, T.Prueksaritanont, C.Shu, M.Torrent, D.C.Heimbrook, N.E.Kohl, H.E.Huber, G.D.Hartman. Kinesin Spindle Protein (Ksp) Inhibitors. Part 2: the Design, Synthesis, and Characterization of 2,4-Diaryl-2,5-Dihydropyrrole Inhibitors of the Mitotic Kinesin Ksp. Bioorg.Med.Chem.Lett. V. 16 1775 2006.
ISSN: ISSN 0960-894X
PubMed: 16439123
DOI: 10.1016/J.BMCL.2006.01.030