Fluorine in PDB 2g1q: Crystal Structure of Ksp in Complex with Inhibitor 9H

The structure of Crystal Structure of Ksp in Complex with Inhibitor 9H, PDB code: 2g1q 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 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.680, 79.640, 158.700, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 27.9

The structure of Crystal Structure of Ksp in Complex with Inhibitor 9H 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 9H (pdb code 2g1q). 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 9H, PDB code: 2g1q:
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 9H


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 9H within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:32.6 occ:1.00 F40 A:N9H604 0.0 32.6 1.0 C4 A:N9H604 1.3 37.5 1.0 C5 A:N9H604 2.3 36.5 1.0 C3 A:N9H604 2.4 39.7 1.0 C14 A:N9H604 2.8 39.1 1.0 C10 A:N9H604 2.9 40.4 1.0 CB A:GLU116 3.5 26.2 1.0 CG2 A:ILE136 3.6 21.9 1.0 C6 A:N9H604 3.6 39.2 1.0 C2 A:N9H604 3.7 40.1 1.0 CB A:ILE136 3.7 23.2 1.0 CG A:GLU116 3.7 27.6 1.0 CA A:GLU116 3.9 24.5 1.0 CD A:PRO137 3.9 26.1 1.0 CD A:GLU116 4.0 29.1 1.0 CD1 A:ILE136 4.0 17.6 1.0 C1 A:N9H604 4.1 41.2 1.0 CD2 A:LEU214 4.1 38.2 1.0 N1 A:N9H604 4.2 40.7 1.0 CD1 A:LEU214 4.2 38.4 1.0 OE2 A:GLU116 4.3 30.4 1.0 C13 A:N9H604 4.3 41.3 1.0 CG1 A:ILE136 4.4 20.0 1.0 OE1 A:GLU116 4.5 31.4 1.0 O A:GLU116 4.5 24.7 1.0 C A:GLU116 4.6 25.6 1.0 N A:PRO137 4.6 26.0 1.0 CG A:LEU214 4.6 38.6 1.0 N12 A:N9H604 4.8 43.3 1.0 CG A:PRO137 4.9 29.1 1.0 CA A:ILE136 4.9 24.0 1.0 CB A:LEU214 4.9 37.8 1.0 C17 A:N9H604 5.0 41.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 9H


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 9H within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:43.3 occ:1.00 F41 A:N9H604 0.0 43.3 1.0 C1 A:N9H604 1.3 41.2 1.0 C6 A:N9H604 2.3 39.2 1.0 C2 A:N9H604 2.3 40.1 1.0 CD2 A:LEU160 3.3 30.1 1.0 CA A:GLY217 3.4 33.9 1.0 C A:GLY217 3.4 32.9 1.0 C5 A:N9H604 3.6 36.5 1.0 C3 A:N9H604 3.6 39.7 1.0 N A:ALA218 3.7 30.3 1.0 O A:GLY217 3.9 31.3 1.0 CZ A:ARG221 4.0 27.0 1.0 NH1 A:ARG221 4.0 29.6 1.0 C4 A:N9H604 4.0 37.5 1.0 NH2 A:ARG221 4.1 26.1 1.0 O A:LEU214 4.2 38.9 1.0 CG A:ARG221 4.3 29.0 1.0 N A:GLY217 4.4 37.0 1.0 NE A:ARG221 4.4 28.8 1.0 CA A:ALA218 4.5 28.8 1.0 CA A:LEU214 4.8 38.4 1.0 OE2 A:GLU116 4.8 30.4 1.0 CG A:LEU160 4.8 29.2 1.0 C10 A:N9H604 4.9 40.4 1.0 CD2 A:LEU172 4.9 43.1 1.0 C A:LEU214 4.9 39.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 9H


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 9H within 5.0Å range: probe atom residue distance (Å) B Occ B:F605 b:37.9 occ:1.00 F40 B:N9H605 0.0 37.9 1.0 C4 B:N9H605 1.3 38.0 1.0 C5 B:N9H605 2.4 36.5 1.0 C3 B:N9H605 2.4 40.0 1.0 C14 B:N9H605 2.8 42.4 1.0 C10 B:N9H605 2.8 41.4 1.0 CG2 B:ILE136 3.6 23.9 1.0 C6 B:N9H605 3.6 39.1 1.0 C2 B:N9H605 3.7 38.9 1.0 CB B:GLU116 3.8 23.8 1.0 CB B:ILE136 3.8 25.6 1.0 CD2 B:LEU214 3.8 30.7 1.0 CD B:PRO137 3.9 24.0 1.0 CG B:GLU116 3.9 24.6 1.0 N1 B:N9H605 4.1 43.4 1.0 C1 B:N9H605 4.1 39.3 1.0 CA B:GLU116 4.1 24.6 1.0 CD1 B:LEU214 4.1 30.2 1.0 CD B:GLU116 4.2 23.8 1.0 CD1 B:ILE136 4.3 23.4 1.0 C13 B:N9H605 4.3 44.4 1.0 O B:GLU116 4.4 21.7 1.0 CG B:LEU214 4.5 32.1 1.0 CG1 B:ILE136 4.6 25.9 1.0 OE1 B:GLU116 4.6 28.2 1.0 N B:PRO137 4.6 24.7 1.0 OE2 B:GLU116 4.7 24.4 1.0 C B:GLU116 4.7 24.3 1.0 CB B:LEU214 4.8 31.3 1.0 N12 B:N9H605 4.8 45.8 1.0 CG B:PRO137 4.8 24.4 1.0 C17 B:N9H605 4.9 42.4 1.0 CA B:ILE136 5.0 25.8 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Ksp in Complex with Inhibitor 9H


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 9H within 5.0Å range: probe atom residue distance (Å) B Occ B:F605 b:42.3 occ:1.00 F41 B:N9H605 0.0 42.3 1.0 C1 B:N9H605 1.3 39.3 1.0 C2 B:N9H605 2.3 38.9 1.0 C6 B:N9H605 2.4 39.1 1.0 C B:GLY217 3.2 26.2 1.0 N B:ALA218 3.2 22.9 1.0 CA B:GLY217 3.3 26.7 1.0 C3 B:N9H605 3.6 40.0 1.0 NH1 B:ARG221 3.7 26.6 1.0 C5 B:N9H605 3.7 36.5 1.0 O B:GLY217 3.7 25.7 1.0 CD2 B:LEU160 3.8 18.9 1.0 O B:LEU214 3.8 33.7 1.0 CZ B:ARG221 3.9 27.3 1.0 CA B:ALA218 4.0 23.9 1.0 CG B:ARG221 4.0 24.4 1.0 C4 B:N9H605 4.1 38.0 1.0 NH2 B:ARG221 4.3 26.1 1.0 NE B:ARG221 4.4 28.2 1.0 N B:GLY217 4.4 28.0 1.0 CB B:ALA218 4.8 20.2 1.0 C B:LEU214 4.8 33.6 1.0 CD B:ARG221 4.8 26.9 1.0 C10 B:N9H605 4.8 41.4 1.0 OE2 B:GLU116 4.9 24.4 1.0 CA B:LEU214 5.0 32.3 1.0

C.D.Cox, M.Torrent, M.J.Breslin, B.J.Mariano, D.B.Whitman, P.J.Coleman, C.A.Buser, E.S.Walsh, K.Hamilton, M.D.Schaber, R.B.Lobell, W.Tao, V.J.South, N.E.Kohl, Y.Yan, L.C.Kuo, T.Prueksaritanont, D.E.Slaughter, C.Li, E.Mahan, B.Lu, G.D.Hartman. Kinesin Spindle Protein (Ksp) Inhibitors. Part 4: Structure-Based Design of 5-Alkylamino-3,5-Diaryl-4,5-Dihydropyrazoles As Potent, Water-Soluble Inhibitors of the Mitotic Kinesin Ksp. Bioorg.Med.Chem.Lett. V. 16 3175 2006.
ISSN: ISSN 0960-894X
PubMed: 16603356
DOI: 10.1016/J.BMCL.2006.03.040