Fluorine in PDB 5stl: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library, PDB code: 5stl was solved by T.Barthel, J.Wollenhaupt, G.M.A.Lima, M.C.Wahl, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.97 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.066, 81.942, 93.69, 90, 108.29, 90
R / Rfree (%)	21.1 / 24.5

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library (pdb code 5stl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library, PDB code: 5stl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.50 F2 B:W9E401 0.0 20.0 0.5 C7 B:W9E401 1.3 20.0 0.5 F B:W9E401 2.0 20.0 0.5 F1 B:W9E401 2.1 20.0 0.5 C2 B:W9E401 2.5 20.0 0.5 HB3 B:TYR68 2.7 46.7 1.0 C3 B:W9E401 2.9 20.0 0.5 HD1 B:PHE89 2.9 55.7 1.0 HG2 B:PRO5 3.0 49.9 1.0 HB2 B:TYR68 3.2 46.7 1.0 CG B:TYR68 3.2 39.6 1.0 CB B:TYR68 3.2 38.9 1.0 CD1 B:TYR68 3.4 42.3 1.0 HE1 B:PHE89 3.4 54.8 1.0 HD1 B:TYR68 3.5 50.7 1.0 HG3 B:PRO5 3.5 49.9 1.0 HB2 B:GLU83 3.7 55.0 1.0 C1 B:W9E401 3.7 20.0 0.5 CD1 B:PHE89 3.7 46.4 1.0 CG B:PRO5 3.7 41.6 1.0 CD2 B:TYR68 3.8 42.6 1.0 CE1 B:PHE89 3.9 45.7 1.0 HG2 B:GLU83 3.9 54.5 1.0 HD2 B:TYR68 4.1 51.1 1.0 CE1 B:TYR68 4.1 45.9 1.0 C4 B:W9E401 4.2 20.0 0.5 HA B:PHE89 4.3 60.2 1.0 HB2 B:PRO5 4.3 47.7 1.0 HG21 B:ILE92 4.4 73.5 1.0 CB B:GLU83 4.4 45.8 1.0 HB3 B:GLU83 4.4 55.0 1.0 CE2 B:TYR68 4.5 39.1 1.0 HD12 B:ILE92 4.5 79.8 1.0 CB B:PRO5 4.6 39.8 1.0 CZ B:TYR68 4.6 45.3 1.0 CA B:TYR68 4.6 35.1 1.0 HE1 B:TYR68 4.6 55.1 1.0 CG B:GLU83 4.6 45.4 1.0 HD2 B:PRO5 4.7 46.8 1.0 C B:W9E401 4.8 20.0 0.5 HG23 B:VAL93 4.8 57.4 1.0 CG B:PHE89 4.9 48.0 1.0 CD B:PRO5 4.9 39.0 1.0 HA B:TYR68 5.0 42.1 1.0 HB B:ILE92 5.0 71.8 1.0 C5 B:W9E401 5.0 20.0 0.5 HG22 B:ILE92 5.0 73.5 1.0

Fluorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.50 F B:W9E401 0.0 20.0 0.5 C7 B:W9E401 1.3 20.0 0.5 F1 B:W9E401 2.0 20.0 0.5 F2 B:W9E401 2.0 20.0 0.5 C2 B:W9E401 2.5 20.0 0.5 HG21 B:ILE92 2.6 73.5 1.0 HD12 B:ILE92 2.7 79.8 1.0 HB B:ILE92 3.0 71.8 1.0 C3 B:W9E401 3.2 20.0 0.5 HA B:PHE89 3.2 60.2 1.0 CG2 B:ILE92 3.3 61.3 1.0 HG22 B:ILE92 3.3 73.5 1.0 C1 B:W9E401 3.4 20.0 0.5 HD1 B:PHE89 3.4 55.7 1.0 CB B:ILE92 3.6 59.9 1.0 CD1 B:ILE92 3.6 66.5 1.0 HG3 B:PRO5 3.8 49.9 1.0 HD13 B:ILE92 3.9 79.8 1.0 HG23 B:VAL93 4.0 57.4 1.0 HG2 B:PRO5 4.1 49.9 1.0 CD1 B:PHE89 4.1 46.4 1.0 HG2 B:GLU83 4.1 54.5 1.0 CG1 B:ILE92 4.1 52.7 1.0 HG23 B:ILE92 4.2 73.5 1.0 CA B:PHE89 4.2 50.1 1.0 HD11 B:ILE92 4.3 79.8 1.0 CG B:PRO5 4.4 41.6 1.0 HG2 B:LYS88 4.4 64.6 1.0 C4 B:W9E401 4.4 20.0 0.5 HB2 B:PRO5 4.4 47.7 1.0 HE2 B:PHE96 4.5 55.6 1.0 HE1 B:PHE89 4.5 54.8 1.0 HG13 B:ILE92 4.5 63.2 1.0 O B:PHE89 4.6 48.3 1.0 HB3 B:TYR68 4.6 46.7 1.0 C B:W9E401 4.6 20.0 0.5 CE1 B:PHE89 4.7 45.7 1.0 O B:LYS88 4.7 50.4 1.0 HE2 B:LYS88 4.8 73.6 1.0 HB2 B:TYR68 4.9 46.7 1.0 HB2 B:GLU83 4.9 55.0 1.0 CG B:PHE89 4.9 48.0 1.0 H B:VAL93 4.9 61.3 1.0 CB B:PRO5 4.9 39.8 1.0 CA B:ILE92 4.9 52.8 1.0 CG2 B:VAL93 4.9 47.9 1.0 N B:PHE89 4.9 48.7 1.0 HB2 B:PHE89 4.9 59.3 1.0 CB B:PHE89 4.9 49.5 1.0 C B:PHE89 5.0 54.0 1.0 C5 B:W9E401 5.0 20.0 0.5 HG12 B:ILE92 5.0 63.2 1.0 H B:ILE92 5.0 69.2 1.0

Fluorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.50 F1 B:W9E401 0.0 20.0 0.5 C7 B:W9E401 1.3 20.0 0.5 F B:W9E401 2.0 20.0 0.5 F2 B:W9E401 2.1 20.0 0.5 C2 B:W9E401 2.4 20.0 0.5 C1 B:W9E401 2.9 20.0 0.5 HB2 B:PRO5 2.9 47.7 1.0 HG2 B:PRO5 2.9 49.9 1.0 HG21 B:ILE92 3.0 73.5 1.0 HE2 B:PHE96 3.1 55.6 1.0 HG3 B:PRO5 3.3 49.9 1.0 CG B:PRO5 3.4 41.6 1.0 HB2 B:TYR68 3.5 46.7 1.0 HG22 B:ILE92 3.5 73.5 1.0 CB B:PRO5 3.6 39.8 1.0 C3 B:W9E401 3.6 20.0 0.5 CG2 B:ILE92 3.7 61.3 1.0 HB3 B:TYR68 3.8 46.7 1.0 CE2 B:PHE96 3.9 46.4 1.0 HD12 B:ILE92 4.0 79.8 1.0 CB B:TYR68 4.0 38.9 1.0 HB3 B:PRO5 4.1 47.7 1.0 HD2 B:TYR68 4.3 51.1 1.0 CG B:TYR68 4.3 39.6 1.0 C B:W9E401 4.3 20.0 0.5 HZ B:PHE96 4.3 63.8 1.0 HG23 B:ILE92 4.3 73.5 1.0 HB B:ILE92 4.4 71.8 1.0 CD2 B:TYR68 4.4 42.6 1.0 HG23 B:VAL93 4.4 57.4 1.0 HD1 B:PHE89 4.5 55.7 1.0 CZ B:PHE96 4.5 53.1 1.0 HD13 B:ILE92 4.6 79.8 1.0 HE1 B:PHE89 4.6 54.8 1.0 C B:PRO5 4.6 33.7 1.0 CB B:ILE92 4.7 59.9 1.0 HG1 B:THR7 4.7 54.5 1.0 HA B:THR7 4.7 44.4 1.0 O B:PRO5 4.7 36.5 1.0 CD1 B:ILE92 4.7 66.5 1.0 CA B:PRO5 4.7 39.9 1.0 HD2 B:PHE96 4.8 63.1 1.0 C4 B:W9E401 4.8 20.0 0.5 CD2 B:PHE96 4.8 52.6 1.0 CD B:PRO5 4.9 39.0 1.0 N B:PHE6 5.0 35.7 1.0 CD1 B:TYR68 5.0 42.3 1.0 H B:PHE6 5.0 42.8 1.0

Fluorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.22 F2 B:W9E402 0.0 20.0 0.2 C7 B:W9E402 1.3 20.0 0.2 F B:W9E402 2.1 20.0 0.2 F1 B:W9E402 2.1 20.0 0.2 C2 B:W9E402 2.4 20.0 0.2 HB2 B:PHE226 2.6 38.4 1.0 HA B:GLU223 2.6 46.5 1.0 HB3 B:PHE226 2.7 38.4 1.0 C3 B:W9E402 2.8 20.0 0.2 CB B:PHE226 3.0 32.0 1.0 HD12 B:ILE129 3.2 50.7 1.0 HD2 B:PHE226 3.2 43.8 1.0 O B:GLY222 3.3 34.4 1.0 CG B:PHE226 3.4 35.4 1.0 CD2 B:PHE226 3.5 36.5 1.0 HG13 B:VAL121 3.5 43.3 1.0 HG12 B:ILE126 3.5 48.4 1.0 CA B:GLU223 3.5 38.7 1.0 C1 B:W9E402 3.5 20.0 0.2 C B:GLY222 3.6 34.4 1.0 N B:GLU223 3.7 38.2 1.0 HA B:ILE126 3.9 50.7 1.0 CD1 B:ILE129 4.0 42.3 1.0 HG13 B:ILE126 4.0 48.4 1.0 HD11 B:ILE129 4.0 50.7 1.0 HB2 B:GLU223 4.1 47.0 1.0 HG22 B:VAL121 4.1 42.4 1.0 H B:PHE226 4.2 40.7 1.0 C4 B:W9E402 4.2 20.0 0.2 CG1 B:ILE126 4.2 40.4 1.0 HA B:VAL121 4.2 45.1 1.0 HD13 B:ILE129 4.2 50.7 1.0 CD1 B:PHE226 4.4 35.1 1.0 CB B:GLU223 4.4 39.2 1.0 CA B:PHE226 4.4 32.9 1.0 H B:GLU223 4.4 45.8 1.0 HB2 B:LYS125 4.4 56.1 1.0 CG1 B:VAL121 4.4 36.1 1.0 HA3 B:GLY222 4.4 45.3 1.0 HG3 B:GLU223 4.5 42.5 1.0 H B:GLN122 4.5 54.0 0.5 H B:GLN122 4.5 54.0 0.5 CE2 B:PHE226 4.5 39.4 1.0 C B:GLU223 4.5 33.2 1.0 O B:GLU223 4.6 34.2 1.0 CA B:ILE126 4.6 42.2 1.0 CA B:GLY222 4.6 37.7 1.0 C B:W9E402 4.7 20.0 0.2 HD1 B:PHE226 4.7 42.1 1.0 N B:PHE226 4.7 33.9 1.0 N B:ILE126 4.7 44.9 1.0 HB3 B:LYS125 4.7 56.1 1.0 HG11 B:VAL121 4.7 43.3 1.0 H B:ILE126 4.8 53.9 1.0 HA B:PHE226 4.9 39.5 1.0 C5 B:W9E402 4.9 20.0 0.2 CG2 B:VAL121 4.9 35.3 1.0 HE2 B:PHE226 4.9 47.3 1.0 HA2 B:GLY222 4.9 45.3 1.0 CG B:GLU223 5.0 35.4 1.0 CB B:ILE126 5.0 39.4 1.0

Fluorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.22 F B:W9E402 0.0 20.0 0.2 C7 B:W9E402 1.3 20.0 0.2 F2 B:W9E402 2.1 20.0 0.2 F1 B:W9E402 2.1 20.0 0.2 C2 B:W9E402 2.4 20.0 0.2 HA B:VAL121 2.4 45.1 1.0 H B:GLN122 2.7 54.0 0.5 H B:GLN122 2.7 54.0 0.5 C1 B:W9E402 2.8 20.0 0.2 HG13 B:VAL121 2.8 43.3 1.0 HA3 B:GLY222 3.2 45.3 1.0 CA B:VAL121 3.3 37.6 1.0 HG22 B:VAL121 3.3 42.4 1.0 C B:GLY222 3.4 34.4 1.0 O B:GLY222 3.4 34.4 1.0 N B:GLN122 3.5 45.0 0.5 N B:GLN122 3.5 45.0 0.5 HB2 B:PHE226 3.6 38.4 1.0 CG1 B:VAL121 3.6 36.1 1.0 C3 B:W9E402 3.6 20.0 0.2 HB2 B:LYS125 3.6 56.1 1.0 CA B:GLY222 3.7 37.7 1.0 O B:PHE120 3.8 37.7 1.0 CB B:VAL121 3.8 40.0 1.0 HA2 B:GLY222 3.9 45.3 1.0 HG13 B:ILE126 3.9 48.4 1.0 C B:VAL121 3.9 39.5 1.0 HA B:GLU223 3.9 46.5 1.0 N B:GLU223 3.9 38.2 1.0 CG2 B:VAL121 4.0 35.3 1.0 HG12 B:VAL121 4.1 43.3 1.0 C B:W9E402 4.1 20.0 0.2 HG12 B:ILE126 4.2 48.4 1.0 HG11 B:VAL121 4.3 43.3 1.0 N B:VAL121 4.3 35.2 1.0 O B:GLN122 4.3 43.9 0.5 O B:GLN122 4.3 43.8 0.5 HG3 B:GLN122 4.4 68.4 0.5 HB3 B:PHE226 4.4 38.4 1.0 CB B:PHE226 4.4 32.0 1.0 C B:PHE120 4.4 36.4 1.0 H B:GLU223 4.4 45.8 1.0 HB3 B:LYS125 4.5 56.1 1.0 CA B:GLU223 4.5 38.7 1.0 CB B:LYS125 4.5 46.7 1.0 CG1 B:ILE126 4.5 40.4 1.0 HB2 B:GLN122 4.6 63.7 0.5 HG21 B:VAL121 4.6 42.4 1.0 H B:ILE126 4.6 53.9 1.0 HG23 B:VAL121 4.7 42.4 1.0 CA B:GLN122 4.7 48.4 0.5 CA B:GLN122 4.7 48.4 0.5 HG2 B:GLN122 4.7 62.3 0.5 C4 B:W9E402 4.8 20.0 0.2 HB B:VAL121 4.8 48.0 1.0 HB2 B:GLN122 4.8 63.5 0.5 HG3 B:LYS125 4.9 72.0 1.0 HA B:ILE126 4.9 50.7 1.0 C B:GLN122 4.9 43.9 0.5 H B:PHE226 4.9 40.7 1.0 C B:GLN122 4.9 43.9 0.5 N B:ILE126 4.9 44.9 1.0 C5 B:W9E402 4.9 20.0 0.2 CG B:PHE226 5.0 35.4 1.0

Fluorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03A02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.22 F1 B:W9E402 0.0 20.0 0.2 C7 B:W9E402 1.3 20.0 0.2 F2 B:W9E402 2.1 20.0 0.2 F B:W9E402 2.1 20.0 0.2 C2 B:W9E402 2.4 20.0 0.2 HG13 B:ILE126 2.5 48.4 1.0 HB2 B:LYS125 2.7 56.1 1.0 H B:ILE126 2.8 53.9 1.0 HG12 B:ILE126 2.8 48.4 1.0 HA B:ILE126 2.8 50.7 1.0 N B:ILE126 2.9 44.9 1.0 C3 B:W9E402 3.1 20.0 0.2 CG1 B:ILE126 3.1 40.4 1.0 H B:GLN122 3.2 54.0 0.5 H B:GLN122 3.2 54.0 0.5 CA B:ILE126 3.2 42.2 1.0 O B:GLN122 3.3 43.9 0.5 O B:GLN122 3.3 43.8 0.5 C1 B:W9E402 3.3 20.0 0.2 C B:LYS125 3.3 46.3 1.0 HG13 B:VAL121 3.3 43.3 1.0 HB3 B:LYS125 3.5 56.1 1.0 CB B:LYS125 3.5 46.7 1.0 CB B:ILE126 3.7 39.4 1.0 O B:LYS125 3.8 42.5 1.0 HD12 B:ILE129 3.9 50.7 1.0 N B:GLN122 4.0 45.0 0.5 N B:GLN122 4.0 45.0 0.5 CA B:LYS125 4.0 51.4 1.0 HA B:VAL121 4.1 45.1 1.0 HB2 B:PHE226 4.1 38.4 1.0 HB B:ILE126 4.2 47.3 1.0 C B:GLN122 4.2 43.9 0.5 C B:GLN122 4.3 43.9 0.5 CG1 B:VAL121 4.3 36.1 1.0 C4 B:W9E402 4.3 20.0 0.2 CD1 B:ILE126 4.4 39.9 1.0 HG12 B:VAL121 4.4 43.3 1.0 H B:LYS125 4.5 60.6 1.0 HD11 B:ILE126 4.5 47.8 1.0 HB2 B:GLN122 4.5 63.7 0.5 C B:W9E402 4.5 20.0 0.2 HB2 B:GLN122 4.6 63.5 0.5 HA B:GLU223 4.6 46.5 1.0 HD2 B:PHE226 4.6 43.8 1.0 CG B:PHE226 4.6 35.4 1.0 CD2 B:PHE226 4.6 36.5 1.0 N B:LYS125 4.7 50.5 1.0 HB3 B:PHE226 4.7 38.4 1.0 C B:ILE126 4.7 41.3 1.0 CA B:GLN122 4.7 48.4 0.5 CA B:GLN122 4.7 48.4 0.5 CB B:PHE226 4.7 32.0 1.0 CG B:LYS125 4.8 60.0 1.0 HG3 B:LYS125 4.8 72.0 1.0 CA B:VAL121 4.8 37.6 1.0 HG11 B:VAL121 4.8 43.3 1.0 HA B:LYS125 4.8 61.7 1.0 C B:VAL121 4.9 39.5 1.0 HD12 B:ILE126 4.9 47.8 1.0 CD1 B:ILE129 4.9 42.3 1.0 C5 B:W9E402 4.9 20.0 0.2 CG2 B:ILE126 4.9 39.8 1.0 HG23 B:ILE126 5.0 47.7 1.0

T.Barthel, J.Wollenhaupt, G.M.A.Lima, M.C.Wahl, M.S.Weiss. Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites. J.Med.Chem. V. 65 14630 2022.
ISSN: ISSN 0022-2623
PubMed: 36260741
DOI: 10.1021/ACS.JMEDCHEM.2C01165