Fluorine in PDB 5wi0: Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One

All present enzymatic activity of Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One:
2.4.2.12;

The structure of Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One, PDB code: 5wi0 was solved by K.L.Longenecker, D.Raich, A.V.Korepanova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.66 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.226, 106.856, 82.881, 90.00, 96.83, 90.00
R / Rfree (%)	21.9 / 24.7

The binding sites of Fluorine atom in the Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One (pdb code 5wi0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One, PDB code: 5wi0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One


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 Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:21.9 occ:1.00 F A:AQ1901 0.0 21.9 1.0 C12 A:AQ1901 1.3 20.2 1.0 C7 A:AQ1901 2.3 17.9 1.0 C11 A:AQ1901 2.4 19.2 1.0 N2 A:AQ1901 2.6 18.6 1.0 OD2 A:ASP219 3.1 25.8 1.0 CB A:ASP219 3.2 16.2 1.0 OD1 B:ASP16 3.3 24.9 1.0 CG B:ASP16 3.4 27.7 1.0 CB B:ASP16 3.4 18.8 1.0 O B:HOH609 3.5 17.8 1.0 CG A:ASP219 3.5 21.4 1.0 CE1 B:TYR18 3.5 15.3 1.0 C8 A:AQ1901 3.6 14.0 1.0 C10 A:AQ1901 3.6 19.4 1.0 CD1 B:TYR18 3.7 13.9 1.0 C6 A:AQ1901 3.9 18.3 1.0 CA A:PHE193 4.0 13.0 1.0 CD1 A:PHE193 4.1 17.6 1.0 C9 A:AQ1901 4.1 18.0 1.0 OD2 B:ASP16 4.1 35.6 1.0 CZ B:TYR18 4.2 18.8 1.0 O B:HOH601 4.2 13.0 1.0 O A:PHE193 4.3 16.9 1.0 CG A:PHE193 4.4 16.2 1.0 CB A:PHE193 4.4 14.4 1.0 CA B:ASP16 4.4 16.1 1.0 N1 A:AQ1901 4.5 17.3 1.0 C A:PHE193 4.5 16.1 1.0 NH2 A:ARG196 4.6 6.2 1.0 CG B:TYR18 4.7 13.7 1.0 CA A:ASP219 4.7 14.0 1.0 OH B:TYR18 4.7 14.6 1.0 OD1 A:ASP219 4.7 21.2 1.0 CE1 A:PHE193 4.8 18.7 1.0 O A:ASP192 4.8 16.6 1.0 N A:AQ1901 4.9 18.1 1.0 CE2 B:TYR18 5.0 14.8 1.0 C B:ASP16 5.0 18.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One


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 Human Nampt with Fragment 2: 2-[(2-Fluorophenyl) Amino]-6-Propylpyrimidin-4(3H)-One within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:21.0 occ:1.00 F B:AQ1501 0.0 21.0 1.0 C12 B:AQ1501 1.3 21.1 1.0 C7 B:AQ1501 2.3 16.9 1.0 C11 B:AQ1501 2.3 21.5 1.0 N2 B:AQ1501 2.7 16.9 1.0 OD2 B:ASP219 3.1 21.9 1.0 CB B:ASP219 3.2 16.1 1.0 OD1 A:ASP16 3.3 19.9 1.0 CG A:ASP16 3.3 21.4 1.0 CB A:ASP16 3.3 16.4 1.0 CE1 A:TYR18 3.5 18.4 1.0 CG B:ASP219 3.5 22.1 1.0 O A:HOH1032 3.6 19.5 1.0 C10 B:AQ1501 3.6 20.2 1.0 C8 B:AQ1501 3.6 13.4 1.0 CD1 A:TYR18 3.8 16.5 1.0 C6 B:AQ1501 4.0 17.6 1.0 CA B:PHE193 4.1 13.2 1.0 C9 B:AQ1501 4.1 18.8 1.0 CD1 B:PHE193 4.1 17.3 1.0 OD2 A:ASP16 4.1 28.4 1.0 O A:HOH1013 4.1 11.1 1.0 CZ A:TYR18 4.2 18.8 1.0 O B:PHE193 4.3 15.7 1.0 CG B:PHE193 4.4 16.1 1.0 CB B:PHE193 4.4 14.4 1.0 CA A:ASP16 4.4 14.8 1.0 NH2 B:ARG196 4.5 12.2 1.0 C B:PHE193 4.5 16.6 1.0 N1 B:AQ1501 4.6 19.2 1.0 CG A:TYR18 4.7 15.2 1.0 CA B:ASP219 4.7 15.3 1.0 OH A:TYR18 4.7 12.1 1.0 OD1 B:ASP219 4.7 21.2 1.0 CE1 B:PHE193 4.8 18.2 1.0 O B:ASP192 4.8 16.7 1.0 C A:ASP16 5.0 17.1 1.0 CE2 A:TYR18 5.0 16.1 1.0 N B:AQ1501 5.0 16.4 1.0

A.Korepanova, K.L.Longenecker, S.D.Pratt, S.C.Panchal, R.F.Clark, M.Lake, S.M.Gopalakrishnan, D.Raich, C.Sun, A.M.Petros. Fragment-Based Discovery of A Potent Nampt Inhibitor. Bioorg. Med. Chem. Lett. V. 28 437 2018.
ISSN: ESSN 1464-3405
PubMed: 29287958
DOI: 10.1016/J.BMCL.2017.12.023