Fluorine in PDB 6hkn: Crystal Structure of Compound 35 with ERK5

All present enzymatic activity of Crystal Structure of Compound 35 with ERK5:
2.7.11.24;

The structure of Crystal Structure of Compound 35 with ERK5, PDB code: 6hkn was solved by D.Nguyen, C.Lemos, L.Wortmann, K.Eis, S.J.Holton, U.Boemer, C.Lechner, S.Prechtl, D.Suelze, F.Siegel, F.Prinz, R.Lesche, B.Nicke, D.Mumberg, M.Bauser, A.Haegebarth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.72 / 2.33
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.488, 92.488, 113.585, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.9

The binding sites of Fluorine atom in the Crystal Structure of Compound 35 with ERK5 (pdb code 6hkn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Compound 35 with ERK5, PDB code: 6hkn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Compound 35 with ERK5


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 Compound 35 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:49.9 occ:1.00 F9 A:G9E1001 0.0 49.9 1.0 C8 A:G9E1001 1.4 41.4 1.0 F11 A:G9E1001 2.3 42.4 1.0 F10 A:G9E1001 2.3 45.1 1.0 O7 A:G9E1001 2.3 37.6 1.0 C6 A:G9E1001 2.9 42.1 1.0 C12 A:G9E1001 3.0 37.2 1.0 CB A:GLU102 3.3 25.1 1.0 OE1 A:GLU102 3.5 30.7 1.0 O A:HOH1110 3.5 54.0 1.0 CD1 A:ILE86 3.6 26.2 1.0 CD A:GLU102 3.6 34.7 1.0 O A:THR99 3.9 32.2 1.0 CG2 A:THR99 4.0 21.4 1.0 CA A:THR99 4.0 23.0 1.0 CG A:GLU102 4.1 27.6 1.0 C5 A:G9E1001 4.1 43.2 1.0 OE2 A:GLU102 4.1 35.5 1.0 C13 A:G9E1001 4.2 42.5 1.0 CB A:THR99 4.4 22.9 1.0 C A:THR99 4.5 26.8 1.0 N A:LEU103 4.5 24.3 1.0 CA A:GLU102 4.6 24.6 1.0 OG1 A:THR99 4.6 20.2 1.0 O A:HOH1180 4.7 49.8 1.0 C A:GLU102 4.7 26.3 1.0 CG A:LEU103 4.8 29.7 1.0 CG1 A:ILE86 4.9 22.2 1.0 N14 A:G9E1001 4.9 36.6 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Compound 35 with ERK5


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 Compound 35 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:45.1 occ:1.00 F10 A:G9E1001 0.0 45.1 1.0 C8 A:G9E1001 1.4 41.4 1.0 F11 A:G9E1001 2.3 42.4 1.0 F9 A:G9E1001 2.3 49.9 1.0 O7 A:G9E1001 2.3 37.6 1.0 CD2 A:LEU103 3.3 27.9 1.0 CG A:LEU103 3.4 29.7 1.0 CD1 A:ILE86 3.4 26.2 1.0 C6 A:G9E1001 3.6 42.1 1.0 CG2 A:THR99 3.6 21.4 1.0 CG2 A:VAL135 3.7 32.3 1.0 O A:THR99 4.1 32.2 1.0 CD1 A:LEU103 4.1 30.6 1.0 C12 A:G9E1001 4.4 37.2 1.0 C5 A:G9E1001 4.4 43.2 1.0 CB A:LEU103 4.6 28.4 1.0 N A:LEU103 4.6 24.3 1.0 CB A:THR99 4.8 22.9 1.0 CA A:LEU103 4.8 28.2 1.0 CG1 A:VAL133 4.8 24.9 1.0 CA A:THR99 4.8 23.0 1.0 CG1 A:ILE86 4.8 22.2 1.0 CB A:VAL135 4.8 31.8 1.0 C A:THR99 4.9 26.8 1.0 CB A:GLU102 4.9 25.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Compound 35 with ERK5


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 Compound 35 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:42.4 occ:1.00 F11 A:G9E1001 0.0 42.4 1.0 C8 A:G9E1001 1.4 41.4 1.0 F10 A:G9E1001 2.3 45.1 1.0 F9 A:G9E1001 2.3 49.9 1.0 O7 A:G9E1001 2.3 37.6 1.0 C6 A:G9E1001 2.8 42.1 1.0 C5 A:G9E1001 3.3 43.2 1.0 N A:LEU103 3.5 24.3 1.0 CB A:GLU102 3.5 25.1 1.0 C A:GLU102 3.7 26.3 1.0 CD2 A:LEU103 3.7 27.9 1.0 C12 A:G9E1001 3.7 37.2 1.0 CG A:LEU103 3.8 29.7 1.0 CA A:LEU103 3.8 28.2 1.0 O A:GLU102 4.0 23.9 1.0 CD1 A:LEU106 4.1 23.4 1.0 CD1 A:ILE117 4.1 32.7 1.0 CA A:GLU102 4.2 24.6 1.0 O A:THR99 4.3 32.2 1.0 CB A:LEU103 4.4 28.4 1.0 C4 A:G9E1001 4.4 42.7 1.0 C13 A:G9E1001 4.7 42.5 1.0 CG A:GLU102 4.8 27.6 1.0 CD A:GLU102 4.8 34.7 1.0 CG2 A:VAL135 4.9 32.3 1.0 CG A:LEU106 4.9 23.6 1.0 CG1 A:ILE117 4.9 31.4 1.0

D.Nguyen, C.Lemos, L.Wortmann, K.Eis, S.J.Holton, U.Boemer, D.Moosmayer, U.Eberspaecher, J.Weiske, C.Lechner, S.Prechtl, D.Suelzle, F.Siegel, F.Prinz, R.Lesche, B.Nicke, K.Nowak-Reppel, H.Himmel, D.Mumberg, F.Von Nussbaum, C.F.Nising, M.Bauser, A.Haegebarth. Discovery and Characterization of the Potent and Highly Selective (Piperidin-4-Yl)Pyrido[3,2- D]Pyrimidine Based in Vitro Probe Bay-885 For the Kinase ERK5. J. Med. Chem. V. 62 928 2019.
ISSN: ISSN 1520-4804
PubMed: 30563338
DOI: 10.1021/ACS.JMEDCHEM.8B01606