Fluorine in PDB 7fkm: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04E03 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04E03 From the F2X-Universal Library, PDB code: 7fkm 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)	44.15 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.043, 81.773, 92.979, 90, 108.26, 90
R / Rfree (%)	21.1 / 23.9

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04E03 From the F2X-Universal Library also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04E03 From the F2X-Universal Library (pdb code 7fkm). 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 P04E03 From the F2X-Universal Library, PDB code: 7fkm:
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 P04E03 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 P04E03 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.34 F1 B:W3B401 0.0 20.0 0.3 C9 B:W3B401 1.2 20.0 0.3 F B:W3B401 1.9 20.0 0.3 O2 B:W3B401 2.0 20.0 0.3 HB2 B:TYR68 2.5 39.3 1.0 HG2 B:PRO5 2.9 47.1 1.0 HB2 B:PRO5 2.9 45.7 1.0 C6 B:W3B401 3.0 20.0 0.3 O B:PRO5 3.1 37.1 1.0 HD2 B:TYR68 3.1 47.5 1.0 C B:PRO5 3.1 33.1 1.0 N B:PHE6 3.3 33.6 1.0 C B:PHE6 3.3 41.3 1.0 N B:THR7 3.3 42.3 1.0 HA B:PHE6 3.3 42.5 1.0 CB B:TYR68 3.4 32.8 1.0 HE2 B:PHE96 3.5 49.9 1.0 CA B:PHE6 3.5 35.5 1.0 H B:THR7 3.5 50.7 1.0 CB B:PRO5 3.6 38.1 1.0 HA B:THR7 3.6 47.5 1.0 H B:PHE6 3.6 40.3 1.0 CG B:PRO5 3.6 39.2 1.0 CD2 B:TYR68 3.6 39.6 1.0 C5 B:W3B401 3.7 20.0 0.3 HB3 B:TYR68 3.7 39.3 1.0 H B:ILE69 3.7 43.9 1.0 O B:PHE6 3.8 39.2 1.0 HG21 B:ILE92 3.8 64.5 1.0 HG1 B:THR7 3.8 47.7 1.0 CG B:TYR68 3.8 37.9 1.0 CA B:THR7 4.0 39.5 1.0 O B:ILE69 4.0 32.8 1.0 CA B:PRO5 4.0 35.6 1.0 OG1 B:THR7 4.0 39.8 1.0 C7 B:W3B401 4.0 20.0 0.3 CL B:W3B401 4.2 20.0 0.3 HG3 B:PRO5 4.2 47.1 1.0 N B:ILE69 4.4 36.6 1.0 HA B:TYR68 4.4 40.5 1.0 CE2 B:PHE96 4.4 41.6 1.0 CA B:TYR68 4.4 33.8 1.0 HB3 B:PRO5 4.4 45.7 1.0 HG22 B:ILE92 4.4 64.5 1.0 CG2 B:ILE92 4.6 53.8 1.0 CB B:THR7 4.6 38.7 1.0 CD B:PRO5 4.7 36.6 1.0 HA B:PRO5 4.7 42.8 1.0 CE2 B:TYR68 4.7 36.2 1.0 HD2 B:PRO5 4.7 44.0 1.0 N B:PRO5 4.8 32.4 1.0 C B:TYR68 4.8 35.2 1.0 C B:ILE69 4.9 34.8 1.0 HG23 B:ILE92 4.9 64.5 1.0 C4 B:W3B401 4.9 20.0 0.3 HE2 B:TYR68 5.0 43.5 1.0 HZ B:PHE96 5.0 65.7 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P04E03 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 P04E03 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.34 F B:W3B401 0.0 20.0 0.3 C9 B:W3B401 1.3 20.0 0.3 F1 B:W3B401 1.9 20.0 0.3 O2 B:W3B401 2.2 20.0 0.3 HE2 B:PHE96 2.4 49.9 1.0 HA B:THR7 2.4 47.5 1.0 HG21 B:ILE92 3.1 64.5 1.0 CA B:THR7 3.2 39.5 1.0 N B:THR7 3.2 42.3 1.0 CE2 B:PHE96 3.2 41.6 1.0 HG1 B:THR7 3.2 47.7 1.0 C B:PHE6 3.2 41.3 1.0 O B:PHE6 3.2 39.2 1.0 C6 B:W3B401 3.2 20.0 0.3 HZ B:PHE96 3.3 65.7 1.0 HB2 B:PRO5 3.4 45.7 1.0 C5 B:W3B401 3.5 20.0 0.3 CZ B:PHE96 3.6 54.8 1.0 OG1 B:THR7 3.7 39.8 1.0 CG2 B:ILE92 3.8 53.8 1.0 H B:THR7 3.8 50.7 1.0 HG23 B:ILE92 3.8 64.5 1.0 HG22 B:ILE92 4.0 64.5 1.0 H B:PHE6 4.0 40.3 1.0 CB B:THR7 4.0 38.7 1.0 N B:PHE6 4.0 33.6 1.0 CA B:PHE6 4.1 35.5 1.0 HG2 B:PRO5 4.2 47.1 1.0 CB B:PRO5 4.3 38.1 1.0 HA B:PHE6 4.3 42.5 1.0 HB2 B:TYR68 4.3 39.3 1.0 C B:THR7 4.3 36.3 1.0 CD2 B:PHE96 4.4 50.2 1.0 C B:PRO5 4.4 33.1 1.0 C7 B:W3B401 4.5 20.0 0.3 HD2 B:TYR68 4.5 47.5 1.0 HD2 B:PHE96 4.5 60.2 1.0 HG23 B:THR7 4.6 63.4 1.0 O B:THR7 4.6 41.7 1.0 HD1 B:HIS31 4.6 66.5 1.0 O B:PRO5 4.7 37.1 1.0 HB B:THR7 4.8 46.5 1.0 CG B:PRO5 4.8 39.2 1.0 HG13 B:ILE92 4.8 65.2 1.0 C4 B:W3B401 4.8 20.0 0.3 CL B:W3B401 4.9 20.0 0.3 HB3 B:PRO5 4.9 45.7 1.0 CG2 B:THR7 4.9 52.9 1.0 CA B:PRO5 5.0 35.6 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