Fluorine in PDB 6hkm: Crystal Structure of Compound 1 with ERK5

All present enzymatic activity of Crystal Structure of Compound 1 with ERK5:
2.7.11.24;

The structure of Crystal Structure of Compound 1 with ERK5, PDB code: 6hkm 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)	70.37 / 2.47
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.477, 92.477, 108.450, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28

The binding sites of Fluorine atom in the Crystal Structure of Compound 1 with ERK5 (pdb code 6hkm). 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 1 with ERK5, PDB code: 6hkm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Compound 1 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 1 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:55.5 occ:1.00 F9 A:G921001 0.0 55.5 1.0 C8 A:G921001 1.4 44.7 1.0 O7 A:G921001 2.2 42.5 1.0 F10 A:G921001 2.3 82.1 1.0 F11 A:G921001 2.3 53.8 1.0 CD1 A:ILE86 3.3 22.0 1.0 C6 A:G921001 3.5 49.9 1.0 CG A:LEU103 3.7 38.4 1.0 CG2 A:VAL135 3.7 27.6 1.0 CG2 A:THR99 3.8 24.9 1.0 O A:THR99 4.1 33.9 1.0 CD1 A:LEU103 4.2 40.7 1.0 C5 A:G921001 4.3 53.3 1.0 CD2 A:LEU103 4.4 43.4 1.0 C12 A:G921001 4.5 52.7 1.0 N A:LEU103 4.7 29.1 1.0 CB A:LEU103 4.7 30.1 1.0 CG1 A:ILE86 4.7 25.8 1.0 CG1 A:VAL133 4.8 29.7 1.0 CA A:LEU103 4.9 27.3 1.0 C A:THR99 4.9 28.4 1.0 CB A:THR99 4.9 23.6 1.0 CB A:VAL135 4.9 28.0 1.0 CA A:THR99 4.9 26.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Compound 1 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 1 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:82.1 occ:1.00 F10 A:G921001 0.0 82.1 1.0 C8 A:G921001 1.4 44.7 1.0 F9 A:G921001 2.3 55.5 1.0 F11 A:G921001 2.3 53.8 1.0 O7 A:G921001 2.3 42.5 1.0 C6 A:G921001 2.8 49.9 1.0 C5 A:G921001 2.9 53.3 1.0 CB A:GLU102 3.3 27.4 1.0 OE2 A:GLU102 3.3 35.6 1.0 CD1 A:ILE86 3.6 22.0 1.0 CD A:GLU102 3.7 29.8 1.0 O A:THR99 3.8 33.9 1.0 C12 A:G921001 4.0 52.7 1.0 O A:HOH1117 4.1 57.6 1.0 CG A:GLU102 4.1 24.9 1.0 CA A:THR99 4.1 26.1 1.0 C4 A:G921001 4.1 55.7 1.0 CG2 A:THR99 4.1 24.9 1.0 N A:LEU103 4.3 29.1 1.0 OE1 A:GLU102 4.3 36.6 1.0 C A:THR99 4.4 28.4 1.0 CA A:GLU102 4.5 29.0 1.0 CB A:THR99 4.6 23.6 1.0 C A:GLU102 4.6 27.1 1.0 OG1 A:THR99 4.8 23.4 1.0 CG1 A:ILE86 4.9 25.8 1.0 C13 A:G921001 4.9 48.9 1.0 O A:ARG98 5.0 26.4 1.0 C3 A:G921001 5.0 42.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Compound 1 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 1 with ERK5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:53.8 occ:1.00 F11 A:G921001 0.0 53.8 1.0 C8 A:G921001 1.4 44.7 1.0 O7 A:G921001 2.3 42.5 1.0 F9 A:G921001 2.3 55.5 1.0 F10 A:G921001 2.3 82.1 1.0 C6 A:G921001 2.9 49.9 1.0 N A:LEU103 3.2 29.1 1.0 C12 A:G921001 3.4 52.7 1.0 CA A:LEU103 3.6 27.3 1.0 CB A:GLU102 3.6 27.4 1.0 C A:GLU102 3.6 27.1 1.0 CG A:LEU103 3.8 38.4 1.0 C5 A:G921001 3.8 53.3 1.0 O A:GLU102 4.1 28.9 1.0 CD1 A:ILE117 4.2 31.0 1.0 CB A:LEU103 4.2 30.1 1.0 O A:THR99 4.2 33.9 1.0 CA A:GLU102 4.3 29.0 1.0 CD2 A:LEU103 4.3 43.4 1.0 CD1 A:LEU106 4.3 23.0 1.0 C13 A:G921001 4.5 48.9 1.0 C4 A:G921001 4.9 55.7 1.0 CG A:GLU102 4.9 24.9 1.0 CD1 A:LEU103 4.9 40.7 1.0 CG1 A:ILE117 4.9 28.7 1.0 C A:LEU103 4.9 26.1 1.0 CG2 A:VAL135 5.0 27.6 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