Fluorine in PDB 4n7e: Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469

The structure of Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469, PDB code: 4n7e was solved by J.L.Andersen, D.Strandbygaard, S.Thirup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.40 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.948, 77.402, 111.176, 90.00, 127.06, 90.00
R / Rfree (%)	20.1 / 24.2

The binding sites of Fluorine atom in the Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469 (pdb code 4n7e). 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 the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469, PDB code: 4n7e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469


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 the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:72.7 occ:1.00 F21 A:2JQ807 0.0 72.7 1.0 C20 A:2JQ807 1.3 72.7 1.0 F23 A:2JQ807 2.2 72.7 1.0 F22 A:2JQ807 2.2 72.7 1.0 C14 A:2JQ807 2.4 72.7 1.0 C13 A:2JQ807 2.7 72.7 1.0 N A:GLY274 2.9 73.6 1.0 C A:PHE273 3.1 78.5 1.0 O A:PHE281 3.4 71.3 1.0 CB A:PHE281 3.4 73.1 1.0 CA A:PHE273 3.4 79.5 1.0 CA A:GLY274 3.5 73.5 1.0 C15 A:2JQ807 3.6 72.7 1.0 O A:PHE273 3.7 78.7 1.0 C A:PHE281 3.7 72.1 1.0 C12 A:2JQ807 4.1 72.7 1.0 N A:PHE273 4.1 81.3 1.0 O A:GLY274 4.2 75.5 1.0 CA A:PHE281 4.2 72.9 1.0 C A:GLY274 4.2 74.7 1.0 CD1 A:ILE320 4.3 50.2 1.0 N A:ALA282 4.4 73.7 1.0 CG A:PHE281 4.6 74.3 1.0 C A:SER272 4.7 81.4 1.0 CB A:PHE273 4.7 79.1 1.0 O A:SER272 4.7 81.0 1.0 CA A:ALA282 4.7 74.0 1.0 C16 A:2JQ807 4.7 72.7 1.0 N A:PHE281 4.9 73.3 1.0 C11 A:2JQ807 4.9 72.7 1.0 CD2 A:PHE281 5.0 75.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469


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 the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:72.7 occ:1.00 F22 A:2JQ807 0.0 72.7 1.0 C20 A:2JQ807 1.3 72.7 1.0 F23 A:2JQ807 2.2 72.7 1.0 F21 A:2JQ807 2.2 72.7 1.0 C14 A:2JQ807 2.4 72.7 1.0 C15 A:2JQ807 2.8 72.7 1.0 N A:SER283 3.2 73.1 1.0 CD1 A:ILE294 3.4 72.4 1.0 C A:ALA282 3.4 75.6 1.0 CA A:ALA282 3.5 74.0 1.0 N A:ALA282 3.5 73.7 1.0 C A:PHE281 3.5 72.1 1.0 C13 A:2JQ807 3.6 72.7 1.0 O A:PHE281 3.7 71.3 1.0 CB A:PHE281 3.7 73.1 1.0 O A:SER272 3.9 81.0 1.0 CB A:SER283 4.0 75.2 1.0 CA A:PHE273 4.1 79.5 1.0 CA A:SER283 4.1 74.8 1.0 OG A:SER283 4.1 75.0 1.0 C16 A:2JQ807 4.2 72.7 1.0 O A:ALA282 4.2 76.3 1.0 CA A:PHE281 4.3 72.9 1.0 C A:SER272 4.3 81.4 1.0 N A:PHE273 4.4 81.3 1.0 C A:PHE273 4.5 78.5 1.0 N A:GLY274 4.6 73.6 1.0 C12 A:2JQ807 4.7 72.7 1.0 CG1 A:ILE294 4.8 73.9 1.0 C11 A:2JQ807 4.9 72.7 1.0 CB A:ALA282 5.0 73.8 1.0 CG A:PHE281 5.0 74.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469


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 the VPS10P Domain of Human Sortilin/NTS3 in Complex with AF38469 within 5.0Å range: probe atom residue distance (Å) B Occ A:F807 b:72.7 occ:1.00 F23 A:2JQ807 0.0 72.7 1.0 C20 A:2JQ807 1.3 72.7 1.0 F21 A:2JQ807 2.2 72.7 1.0 F22 A:2JQ807 2.2 72.7 1.0 C14 A:2JQ807 2.3 72.7 1.0 C13 A:2JQ807 3.1 72.7 1.0 C15 A:2JQ807 3.1 72.7 1.0 CB A:PHE281 3.4 73.1 1.0 CD1 A:ILE294 3.5 72.4 1.0 CG A:PHE281 4.1 74.3 1.0 CD1 A:ILE320 4.1 50.2 1.0 C12 A:2JQ807 4.3 72.7 1.0 CG1 A:ILE320 4.3 50.1 1.0 C16 A:2JQ807 4.3 72.7 1.0 CE A:MET330 4.4 61.9 1.0 C A:PHE281 4.5 72.1 1.0 CA A:PHE281 4.6 72.9 1.0 CD2 A:PHE281 4.6 75.0 1.0 CB A:TYR318 4.7 59.5 1.0 CG1 A:ILE294 4.7 73.9 1.0 SD A:MET330 4.7 60.4 1.0 O A:PHE281 4.7 71.3 1.0 C11 A:2JQ807 4.8 72.7 1.0 CD1 A:PHE281 4.8 75.0 1.0 N A:ALA282 4.9 73.7 1.0 N A:GLY274 5.0 73.6 1.0

T.J.Schrder, S.Christensen, S.Lindberg, M.Langgard, L.David, P.J.Maltas, J.Eskildsen, J.Jacobsen, L.Tagmose, K.B.Simonsen, L.C.Biilmann Rnn, I.E.De Jong, I.J.Malik, J.J.Karlsson, C.Bundgaard, J.Egebjerg, J.B.Stavenhagen, D.Strandbygard, S.Thirup, J.L.Andersen, S.Uppalanchi, S.Pervaram, S.P.Kasturi, P.Eradi, D.R.Sakumudi, S.P.Watson. The Identification of AF38469: An Orally Bioavailable Inhibitor of the VPS10P Family Sorting Receptor Sortilin. Bioorg.Med.Chem.Lett. V. 24 177 2014.
ISSN: ISSN 0960-894X
PubMed: 24355129
DOI: 10.1016/J.BMCL.2013.11.046