Fluorine in PDB 5nad: Ttk Kinase Domain in Complex with Bay 1217389

All present enzymatic activity of Ttk Kinase Domain in Complex with Bay 1217389:
2.7.12.1;

The structure of Ttk Kinase Domain in Complex with Bay 1217389, PDB code: 5nad was solved by J.C.M.Uitdehaag, N.Willemsen-Seegers, J.G.Sterrenburg, J.De Man, R.C.Buijsman, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.19 / 2.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.450, 109.780, 114.330, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 29

The binding sites of Fluorine atom in the Ttk Kinase Domain in Complex with Bay 1217389 (pdb code 5nad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Ttk Kinase Domain in Complex with Bay 1217389, PDB code: 5nad:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Ttk Kinase Domain in Complex with Bay 1217389


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ttk Kinase Domain in Complex with Bay 1217389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:0.3 occ:1.00 F36 A:8RH901 0.0 0.3 1.0 C20 A:8RH901 1.3 86.3 1.0 C21 A:8RH901 2.4 82.4 1.0 C22 A:8RH901 2.5 83.8 1.0 C38 A:8RH901 2.6 92.5 1.0 O37 A:8RH901 2.8 90.5 1.0 F35 A:8RH901 2.9 0.8 1.0 O A:ALA651 3.0 87.5 1.0 C A:ALA651 3.3 86.4 1.0 CB A:ALA651 3.5 83.5 1.0 C24 A:8RH901 3.7 81.6 1.0 C19 A:8RH901 3.7 74.8 1.0 N A:ASN652 3.9 76.0 1.0 CA A:ALA651 4.0 79.2 1.0 CD1 A:ILE663 4.0 76.5 1.0 CA A:ASN652 4.1 74.1 1.0 C23 A:8RH901 4.2 65.9 1.0 CD A:PRO673 4.3 87.4 1.0 ND2 A:ASN652 4.3 64.1 1.0 CG A:PRO673 4.6 97.1 1.0 O18 A:8RH901 4.7 75.6 1.0 C30 A:8RH901 4.8 63.7 1.0

Fluorine binding site 2 out of 5 in the Ttk Kinase Domain in Complex with Bay 1217389


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ttk Kinase Domain in Complex with Bay 1217389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:0.8 occ:1.00 F35 A:8RH901 0.0 0.8 1.0 C21 A:8RH901 1.3 82.4 1.0 C19 A:8RH901 2.3 74.8 1.0 C20 A:8RH901 2.4 86.3 1.0 O18 A:8RH901 2.5 75.6 1.0 F36 A:8RH901 2.9 0.3 1.0 C1 A:8RH901 3.0 66.6 1.0 O A:ALA651 3.1 87.5 1.0 N5 A:8RH901 3.6 59.5 1.0 C23 A:8RH901 3.6 65.9 1.0 CB A:ASP608 3.7 93.4 1.0 C22 A:8RH901 3.7 83.8 1.0 CD1 A:ILE663 3.7 76.5 1.0 OD2 A:ASP608 3.7 0.7 1.0 CG A:PRO673 3.7 97.1 1.0 C3 A:8RH901 3.8 64.0 1.0 C A:ALA651 4.1 86.4 1.0 C24 A:8RH901 4.1 81.6 1.0 CG A:ASP608 4.1 0.6 1.0 CB A:ALA651 4.4 83.5 1.0 CA A:ALA651 4.4 79.2 1.0 CD A:PRO673 4.4 87.4 1.0 CB A:PRO673 4.7 96.3 1.0 N6 A:8RH901 4.7 58.6 1.0 O37 A:8RH901 4.8 90.5 1.0 O A:PHE653 4.8 71.1 1.0 C2 A:8RH901 4.9 72.9 1.0

Fluorine binding site 3 out of 5 in the Ttk Kinase Domain in Complex with Bay 1217389


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ttk Kinase Domain in Complex with Bay 1217389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:0.6 occ:1.00 F16 A:8RH901 0.0 0.6 1.0 C13 A:8RH901 1.3 94.2 1.0 F15 A:8RH901 2.2 83.8 1.0 F14 A:8RH901 2.2 93.4 1.0 C12 A:8RH901 2.3 90.8 1.0 NE2 A:GLN541 3.5 83.0 1.0 O A:ASN606 3.6 0.5 1.0 C11 A:8RH901 3.6 90.0 1.0 CD A:GLN541 4.2 72.8 1.0 NZ A:LYS529 4.2 94.3 1.0 OE1 A:GLN541 4.3 80.5 1.0 O A:GLY605 4.5 98.4 1.0 N10 A:8RH901 4.5 82.8 1.0 C A:ASN606 4.7 98.9 1.0 CE A:LYS529 4.8 81.2 1.0 SG A:CYS604 5.0 90.8 1.0

Fluorine binding site 4 out of 5 in the Ttk Kinase Domain in Complex with Bay 1217389


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ttk Kinase Domain in Complex with Bay 1217389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:83.8 occ:1.00 F15 A:8RH901 0.0 83.8 1.0 C13 A:8RH901 1.3 94.2 1.0 F16 A:8RH901 2.2 0.6 1.0 F14 A:8RH901 2.2 93.4 1.0 C12 A:8RH901 2.3 90.8 1.0 NE2 A:GLN541 2.9 83.0 1.0 C11 A:8RH901 2.9 90.0 1.0 CD A:GLN541 3.0 72.8 1.0 OE1 A:GLN541 3.3 80.5 1.0 CG A:GLN541 3.7 71.6 1.0 CB A:GLN541 3.8 76.0 1.0 SG A:CYS604 3.8 90.8 1.0 CG2 A:ILE531 3.9 88.4 1.0 N10 A:8RH901 4.2 82.8 1.0 NZ A:LYS529 4.3 94.3 1.0 CE A:LYS529 4.4 81.2 1.0 CD1 A:ILE531 4.4 74.8 1.0 O A:GLY605 4.7 98.4 1.0 CB A:ILE531 4.7 79.0 1.0 CA A:GLN541 5.0 73.1 1.0 C2 A:8RH901 5.0 72.9 1.0

Fluorine binding site 5 out of 5 in the Ttk Kinase Domain in Complex with Bay 1217389


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ttk Kinase Domain in Complex with Bay 1217389 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:93.4 occ:1.00 F14 A:8RH901 0.0 93.4 1.0 C13 A:8RH901 1.3 94.2 1.0 F15 A:8RH901 2.2 83.8 1.0 F16 A:8RH901 2.2 0.6 1.0 C12 A:8RH901 2.3 90.8 1.0 C11 A:8RH901 2.8 90.0 1.0 N10 A:8RH901 3.3 82.8 1.0 NZ A:LYS529 3.9 94.3 1.0 CG2 A:ILE531 4.2 88.4 1.0 C2 A:8RH901 4.2 72.9 1.0 CB A:ILE531 4.4 79.0 1.0 O A:ASN606 4.5 0.5 1.0 C3 A:8RH901 4.6 64.0 1.0 CE A:LYS529 4.7 81.2 1.0 NE2 A:GLN541 4.8 83.0 1.0 CD1 A:ILE531 4.9 74.8 1.0 OE1 A:GLN541 5.0 80.5 1.0

J.C.M.Uitdehaag, J.De Man, N.Willemsen-Seegers, M.B.W.Prinsen, M.A.A.Libouban, J.G.Sterrenburg, J.J.P.De Wit, J.R.F.De Vetter, J.A.D.M.De Roos, R.C.Buijsman, G.J.R.Zaman. Target Residence Time-Guided Optimization on Ttk Kinase Results in Inhibitors with Potent Anti-Proliferative Activity. J. Mol. Biol. V. 429 2211 2017.
ISSN: ESSN 1089-8638
PubMed: 28539250
DOI: 10.1016/J.JMB.2017.05.014