Fluorine in PDB 3cjo: Crystal Structure of Ksp in Complex with Inhibitor 30

The structure of Crystal Structure of Ksp in Complex with Inhibitor 30, PDB code: 3cjo 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 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.758, 79.374, 158.853, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 26.1

The structure of Crystal Structure of Ksp in Complex with Inhibitor 30 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 30 (pdb code 3cjo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Ksp in Complex with Inhibitor 30, PDB code: 3cjo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:27.4 occ:1.00 F13 A:K301 0.0 27.4 1.0 C8 A:K301 1.3 28.2 1.0 C9 A:K301 2.3 31.0 1.0 C7 A:K301 2.3 29.1 1.0 N A:ALA218 3.3 31.7 1.0 C A:GLY217 3.4 33.9 1.0 NH1 A:ARG221 3.5 22.9 1.0 CA A:GLY217 3.6 30.4 1.0 C6 A:K301 3.6 31.7 1.0 C4 A:K301 3.7 31.3 1.0 CD2 A:LEU160 3.7 35.8 1.0 O A:LEU214 3.8 35.7 1.0 CZ A:ARG221 3.9 39.0 1.0 O A:GLY217 3.9 31.7 1.0 CA A:ALA218 4.0 30.7 1.0 C5 A:K301 4.1 30.3 1.0 NE A:ARG221 4.3 26.4 1.0 NH2 A:ARG221 4.4 41.0 1.0 CD A:ARG221 4.4 31.0 1.0 N A:GLY217 4.5 30.4 1.0 CB A:ALA218 4.6 30.8 1.0 CA A:LEU214 4.6 28.6 1.0 C A:LEU214 4.6 35.2 1.0 C3 A:K301 4.8 35.0 1.0 OE2 A:GLU116 4.8 38.2 1.0 C A:K301 4.8 38.2 1.0 CG A:ARG221 4.9 24.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:32.3 occ:1.00 F A:K301 0.0 32.3 1.0 C5 A:K301 1.3 30.3 1.0 C6 A:K301 2.3 31.7 1.0 C4 A:K301 2.4 31.3 1.0 CB A:GLU116 3.0 19.8 1.0 C3 A:K301 3.0 35.0 1.0 C2 A:K301 3.1 37.6 1.0 CA A:GLU116 3.5 18.6 1.0 CG A:GLU116 3.5 23.4 1.0 CB A:ILE136 3.6 30.5 1.0 C7 A:K301 3.6 29.1 1.0 CD A:PRO137 3.7 30.0 1.0 C9 A:K301 3.7 31.0 1.0 CG2 A:ILE136 3.8 31.1 1.0 CD A:GLU116 3.9 35.3 1.0 C8 A:K301 4.1 28.2 1.0 CD1 A:ILE136 4.1 26.0 1.0 CD2 A:LEU214 4.2 31.4 1.0 OE2 A:GLU116 4.2 38.2 1.0 O A:GLU116 4.3 23.3 1.0 C A:GLU116 4.3 25.6 1.0 O A:MET115 4.4 28.2 1.0 CG1 A:ILE136 4.4 30.0 1.0 OE1 A:GLU116 4.4 41.6 1.0 C A:K301 4.4 38.2 1.0 N A:GLU116 4.5 19.3 1.0 CD1 A:LEU214 4.6 28.6 1.0 N A:PRO137 4.6 28.1 1.0 CG A:PRO137 4.6 34.9 1.0 C1 A:K301 4.6 41.5 1.0 CA A:ILE136 4.6 28.9 1.0 C A:MET115 4.9 25.8 1.0 C A:ILE136 4.9 31.7 1.0 CG A:LEU214 4.9 30.6 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:53.5 occ:1.00 F29 A:K301 0.0 53.5 1.0 C23 A:K301 1.4 54.1 1.0 C24 A:K301 2.3 59.2 1.0 C12 A:K301 2.3 50.7 1.0 N25 A:K301 2.6 63.5 1.0 C27 A:K301 2.8 57.8 1.0 O A:HOH673 2.8 40.7 1.0 N11 A:K301 2.9 38.5 1.0 C22 A:K301 3.0 35.8 1.0 C26 A:K301 3.2 61.4 1.0 CA A:GLU215 3.5 33.8 1.0 CB A:ALA218 3.5 30.8 1.0 O A:GLU215 3.8 30.9 1.0 C28 A:K301 3.9 66.2 1.0 CB A:GLU215 4.1 35.6 1.0 CG A:GLU215 4.1 49.6 1.0 C A:GLU215 4.1 34.5 1.0 C10 A:K301 4.2 42.1 1.0 OE1 A:GLU215 4.4 48.5 1.0 O A:LEU214 4.4 35.7 1.0 N A:GLU215 4.5 34.7 1.0 CD A:GLU215 4.7 75.9 1.0 C A:LEU214 4.8 35.2 1.0 CA A:ALA218 4.9 30.7 1.0 O A:HOH727 5.0 39.4 1.0 O A:K301 5.0 44.0 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


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 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:32.3 occ:1.00 F13 B:K30603 0.0 32.3 1.0 C8 B:K30603 1.3 26.4 1.0 C9 B:K30603 2.3 27.7 1.0 C7 B:K30603 2.3 26.7 1.0 N B:ALA218 3.3 29.6 1.0 C B:GLY217 3.4 32.4 1.0 C4 B:K30603 3.6 34.6 1.0 C6 B:K30603 3.6 30.7 1.0 CA B:GLY217 3.7 31.1 1.0 CZ B:ARG221 3.8 54.8 1.0 O B:LEU214 3.9 31.9 1.0 NE B:ARG221 3.9 47.3 1.0 CD2 B:LEU160 3.9 27.8 1.0 CA B:ALA218 4.0 29.7 1.0 NH2 B:ARG221 4.1 63.0 1.0 C5 B:K30603 4.1 31.6 1.0 O B:GLY217 4.1 30.9 1.0 NH1 B:ARG221 4.3 27.7 1.0 CD B:ARG221 4.4 33.2 1.0 CB B:ALA218 4.6 29.1 1.0 N B:GLY217 4.6 31.4 1.0 OE1 B:GLU116 4.7 19.4 1.0 OE2 B:GLU116 4.7 29.9 1.0 C3 B:K30603 4.7 39.5 1.0 C B:LEU214 4.8 33.6 1.0 CA B:LEU214 4.8 32.6 1.0 C B:K30603 4.9 41.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Ksp in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:34.0 occ:1.00 F B:K30603 0.0 34.0 1.0 C5 B:K30603 1.3 31.6 1.0 C4 B:K30603 2.3 34.6 1.0 C6 B:K30603 2.4 30.7 1.0 C3 B:K30603 2.8 39.5 1.0 C2 B:K30603 2.9 44.8 1.0 CB B:GLU116 2.9 21.4 1.0 CA B:GLU116 3.5 21.7 1.0 CD B:PRO137 3.6 28.6 1.0 C9 B:K30603 3.6 27.7 1.0 CG B:GLU116 3.7 21.6 1.0 C7 B:K30603 3.7 26.7 1.0 CB B:ILE136 3.8 30.3 1.0 CD B:GLU116 3.9 29.6 1.0 CD1 B:LEU214 4.0 32.6 1.0 C8 B:K30603 4.1 26.4 1.0 CG2 B:ILE136 4.1 25.4 1.0 O B:GLU116 4.2 24.9 1.0 C B:GLU116 4.2 26.7 1.0 C B:K30603 4.2 41.8 1.0 OE1 B:GLU116 4.3 19.4 1.0 OE2 B:GLU116 4.3 29.9 1.0 CG B:PRO137 4.3 33.2 1.0 C1 B:K30603 4.4 49.2 1.0 CD1 B:ILE136 4.5 18.2 1.0 O B:MET115 4.5 30.2 1.0 N B:PRO137 4.6 26.1 1.0 CG1 B:ILE136 4.7 31.1 1.0 N B:GLU116 4.7 24.0 1.0 CD2 B:LEU214 4.8 33.7 1.0 CG B:LEU214 4.9 33.7 1.0 CA B:ILE136 4.9 29.1 1.0 N B:K30603 4.9 47.8 1.0 C15 B:K30603 5.0 45.6 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Ksp in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Ksp in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:64.5 occ:1.00 F29 B:K30603 0.0 64.5 1.0 C23 B:K30603 1.4 61.5 1.0 C12 B:K30603 2.2 58.1 1.0 C24 B:K30603 2.2 64.5 1.0 N25 B:K30603 2.3 64.9 1.0 C27 B:K30603 2.5 61.9 1.0 N11 B:K30603 2.7 50.9 1.0 C26 B:K30603 2.8 64.8 1.0 O B:HOH746 2.9 62.9 1.0 C22 B:K30603 2.9 46.1 1.0 CB B:ALA218 3.0 29.1 1.0 C28 B:K30603 3.6 64.6 1.0 CA B:GLU215 3.8 31.6 1.0 C10 B:K30603 3.9 47.7 1.0 O B:GLU215 4.1 38.3 1.0 CG B:GLU215 4.4 47.8 1.0 O B:LEU214 4.4 31.9 1.0 C B:GLU215 4.5 35.5 1.0 CA B:ALA218 4.5 29.7 1.0 CB B:GLU215 4.5 33.1 1.0 N B:K30603 4.6 47.8 1.0 C B:K30603 4.6 41.8 1.0 O B:K30603 4.6 46.8 1.0 N B:GLU215 4.7 31.3 1.0 C B:LEU214 4.9 33.6 1.0 C B:ALA218 5.0 37.8 1.0

C.D.Cox, P.J.Coleman, M.J.Breslin, D.B.Whitman, R.M.Garbaccio, M.E.Fraley, C.A.Buser, E.S.Walsh, K.Hamilton, M.D.Schaber, R.B.Lobell, W.Tao, J.P.Davide, R.E.Diehl, M.T.Abrams, V.J.South, H.E.Huber, M.Torrent, T.Prueksaritanont, C.Li, D.E.Slaughter, E.Mahan, C.Fernandez-Metzler, Y.Yan, L.C.Kuo, N.E.Kohl, G.D.Hartman. Kinesin Spindle Protein (Ksp) Inhibitors. 9. Discovery of (2S)-4-(2,5-Difluorophenyl)-N-[(3R,4S)-3-Fluoro-1- Methylpiperidin-4-Yl]-2-(Hydroxymethyl)-N-Methyl-2- Phenyl-2,5-Dihydro-1H-Pyrrole-1-Carboxamide (Mk-0731) For the Treatment of Taxane-Refractory Cancer. J.Med.Chem. V. 51 4239 2008.
ISSN: ISSN 0022-2623
PubMed: 18578472
DOI: 10.1021/JM800386Y