Fluorine in PDB 7fki: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 From the F2X-Universal Library, PDB code: 7fki 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)	44.36 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.867, 81.763, 93.657, 90, 108.68, 90
R / Rfree (%)	20.2 / 23.6

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 From the F2X-Universal Library (pdb code 7fki). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 From the F2X-Universal Library, PDB code: 7fki:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 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 P04D08 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:30.0 occ:1.00 F1 B:W25501 0.0 30.0 1.0 C2 B:W25501 1.3 30.0 1.0 C3 B:W25501 2.3 30.0 1.0 C1 B:W25501 2.3 30.0 1.0 H2 B:W25501 2.6 30.0 1.0 F B:W25501 2.6 30.0 1.0 HD1 B:PHE89 2.7 38.7 1.0 HB3 B:TYR68 3.0 28.1 1.0 HG2 B:PRO5 3.2 35.7 1.0 HD12 B:ILE92 3.3 63.0 1.0 CG B:TYR68 3.3 24.9 1.0 HE1 B:PHE89 3.3 35.3 1.0 CD1 B:TYR68 3.3 25.9 1.0 CD1 B:PHE89 3.4 32.2 1.0 HD1 B:TYR68 3.5 31.1 1.0 HB2 B:GLU83 3.5 36.8 1.0 HG21 B:ILE92 3.5 44.3 1.0 CB B:TYR68 3.5 23.4 1.0 C4 B:W25501 3.6 30.0 1.0 C B:W25501 3.6 30.0 1.0 HB2 B:TYR68 3.7 28.1 1.0 HG2 B:GLU83 3.7 44.5 1.0 CE1 B:PHE89 3.8 29.4 1.0 CD2 B:TYR68 3.8 27.7 1.0 CE1 B:TYR68 3.9 28.1 1.0 C5 B:W25501 4.1 30.0 1.0 HA B:PHE89 4.1 39.4 1.0 CG B:PRO5 4.1 29.8 1.0 CD1 B:ILE92 4.1 52.5 1.0 HG3 B:PRO5 4.1 35.7 1.0 HD13 B:ILE92 4.2 63.0 1.0 HD2 B:TYR68 4.2 33.2 1.0 CB B:GLU83 4.2 30.7 1.0 HB3 B:GLU83 4.2 36.8 1.0 CE2 B:TYR68 4.3 28.3 1.0 CG2 B:ILE92 4.4 36.9 1.0 HE1 B:TYR68 4.4 33.7 1.0 HB B:ILE92 4.4 41.0 1.0 CZ B:TYR68 4.4 26.9 1.0 CG B:GLU83 4.4 37.1 1.0 H3 B:W25501 4.5 30.0 1.0 HG22 B:ILE92 4.5 44.3 1.0 H1 B:W25501 4.5 30.0 1.0 CG B:PHE89 4.6 28.4 1.0 HE3 B:LYS88 4.6 60.5 1.0 HB2 B:PRO5 4.7 31.7 1.0 HD11 B:ILE92 4.7 63.0 1.0 HB2 B:PHE89 4.7 37.4 1.0 HD2 B:PRO5 4.8 28.9 1.0 CB B:ILE92 4.8 34.1 1.0 OE1 B:GLU83 4.9 37.4 1.0 CA B:PHE89 5.0 32.8 1.0 HE2 B:TYR68 5.0 34.0 1.0 CA B:TYR68 5.0 22.7 1.0 CB B:PRO5 5.0 26.4 1.0 CB B:PHE89 5.0 31.2 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04D08 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 P04D08 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:30.0 occ:1.00 F B:W25501 0.0 30.0 1.0 C3 B:W25501 1.3 30.0 1.0 C2 B:W25501 2.3 30.0 1.0 C4 B:W25501 2.3 30.0 1.0 H3 B:W25501 2.6 30.0 1.0 F1 B:W25501 2.6 30.0 1.0 HG21 B:ILE92 2.6 44.3 1.0 HG2 B:PRO5 2.7 35.7 1.0 HB2 B:PRO5 2.8 31.7 1.0 HB2 B:TYR68 3.1 28.1 1.0 HE2 B:PHE96 3.4 37.2 1.0 CG B:PRO5 3.5 29.8 1.0 CG2 B:ILE92 3.5 36.9 1.0 CB B:PRO5 3.5 26.4 1.0 HB3 B:TYR68 3.5 28.1 1.0 HD2 B:TYR68 3.5 33.2 1.0 C1 B:W25501 3.5 30.0 1.0 C5 B:W25501 3.6 30.0 1.0 CB B:TYR68 3.6 23.4 1.0 HG22 B:ILE92 3.7 44.3 1.0 CD2 B:TYR68 3.8 27.7 1.0 HG23 B:ILE92 3.8 44.3 1.0 HG3 B:PRO5 3.8 35.7 1.0 CG B:TYR68 3.8 24.9 1.0 HG1 B:THR7 3.9 38.6 1.0 HD12 B:ILE92 4.0 63.0 1.0 C B:W25501 4.0 30.0 1.0 HB3 B:PRO5 4.1 31.7 1.0 HD13 B:ILE92 4.2 63.0 1.0 C B:PRO5 4.3 25.4 1.0 HA B:THR7 4.3 35.8 1.0 CE2 B:PHE96 4.3 31.0 1.0 O B:PRO5 4.4 25.9 1.0 H2 B:W25501 4.4 30.0 1.0 CD1 B:ILE92 4.5 52.5 1.0 CA B:PRO5 4.5 23.7 1.0 N B:PHE6 4.6 24.6 1.0 N B:THR7 4.6 27.9 1.0 C B:PHE6 4.6 27.1 1.0 CE2 B:TYR68 4.6 28.3 1.0 H B:THR7 4.6 33.5 1.0 H B:PHE6 4.7 29.6 1.0 CB B:ILE92 4.7 34.1 1.0 HE1 B:PHE89 4.7 35.3 1.0 HD2 B:PHE96 4.7 41.5 1.0 CD B:PRO5 4.7 24.1 1.0 CD1 B:TYR68 4.7 25.9 1.0 HB B:ILE92 4.7 41.0 1.0 HD2 B:PRO5 4.8 28.9 1.0 OG1 B:THR7 4.8 32.2 1.0 O B:PHE6 4.9 28.4 1.0 C6 B:W25501 4.9 30.0 1.0 HD1 B:PHE89 4.9 38.7 1.0 CA B:THR7 4.9 29.8 1.0 HE2 B:TYR68 4.9 34.0 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