Fluorine in PDB 6r9s: Human Cyclophilin D in Complex with Bicyclic Fragment

All present enzymatic activity of Human Cyclophilin D in Complex with Bicyclic Fragment:
5.2.1.8;

The structure of Human Cyclophilin D in Complex with Bicyclic Fragment, PDB code: 6r9s was solved by U.Graedler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.382, 57.382, 88.119, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.8

The binding sites of Fluorine atom in the Human Cyclophilin D in Complex with Bicyclic Fragment (pdb code 6r9s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Cyclophilin D in Complex with Bicyclic Fragment, PDB code: 6r9s:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Human Cyclophilin D in Complex with Bicyclic Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Cyclophilin D in Complex with Bicyclic Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:14.4 occ:1.00 F7 A:JVN301 0.0 14.4 1.0 C1 A:JVN301 1.3 12.7 1.0 C6 A:JVN301 2.4 11.7 1.0 C2 A:JVN301 2.4 10.7 1.0 O A:HOH497 2.9 23.0 1.0 O A:GLY114 3.2 14.9 1.0 C5 A:JVN301 3.6 11.9 1.0 C3 A:JVN301 3.6 10.2 1.0 O A:ASN144 3.9 10.3 1.0 NE2 A:GLN153 4.1 11.4 1.0 CB A:ALA145 4.1 12.6 1.0 C4 A:JVN301 4.1 9.4 1.0 C A:ASN144 4.2 12.0 1.0 OE1 A:GLN153 4.4 8.5 1.0 C A:GLY114 4.4 15.5 1.0 CD A:GLN153 4.5 18.1 1.0 N A:ALA145 4.5 10.8 1.0 C2 A:JVN302 4.5 14.4 1.0 CA A:ALA145 4.6 11.8 1.0 F7 A:JVN302 4.7 15.7 1.0 C1 A:JVN302 4.7 14.6 1.0 C8 A:JVN301 4.9 12.9 1.0 O A:HOH575 4.9 47.8 1.0 CA A:ASN144 5.0 8.2 1.0 NE2 A:GLN105 5.0 7.4 1.0

Fluorine binding site 2 out of 2 in the Human Cyclophilin D in Complex with Bicyclic Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Cyclophilin D in Complex with Bicyclic Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:15.7 occ:1.00 F7 A:JVN302 0.0 15.7 1.0 C1 A:JVN302 1.3 14.6 1.0 C6 A:JVN302 2.4 13.9 1.0 C2 A:JVN302 2.4 14.4 1.0 O A:THR115 3.2 16.2 1.0 CA A:THR115 3.2 11.7 1.0 C6 A:JVN301 3.6 11.7 1.0 C5 A:JVN302 3.6 15.8 1.0 C A:THR115 3.6 16.0 1.0 C3 A:JVN302 3.6 16.1 1.0 CB A:THR115 3.7 16.0 1.0 C8 A:JVN301 3.9 12.9 1.0 O12 A:JVN301 4.1 13.5 1.0 C4 A:JVN302 4.1 17.4 1.0 O A:GLY114 4.1 14.9 1.0 CG2 A:THR115 4.1 14.3 1.0 C5 A:JVN301 4.2 11.9 1.0 N A:THR115 4.4 12.1 1.0 C1 A:JVN301 4.6 12.7 1.0 F7 A:JVN301 4.7 14.4 1.0 C A:GLY114 4.7 15.5 1.0 C8 A:JVN302 4.9 17.6 1.0 N A:GLY116 4.9 11.9 1.0 OG1 A:THR115 5.0 9.3 1.0

U.Gradler, D.Schwarz, M.Blaesse, B.Leuthner, T.L.Johnson, F.Bernard, X.Jiang, A.Marx, M.Gilardone, H.Lemoine, D.Roche, C.Jorand-Lebrun. Discovery of Novel Cyclophilin D Inhibitors Starting From Three Dimensional Fragments with Millimolar Potencies. Bioorg.Med.Chem.Lett. V. 29 26717 2019.
ISSN: ESSN 1464-3405
PubMed: 31635932
DOI: 10.1016/J.BMCL.2019.126717