Fluorine in PDB 7fog: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 From the F2X-Universal Library, PDB code: 7fog 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)	44.48 / 1.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.235, 81.918, 93.612, 90, 108.13, 90
R / Rfree (%)	21.3 / 24

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 From the F2X-Universal Library (pdb code 7fog). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 From the F2X-Universal Library, PDB code: 7fog:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 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 P08B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.60 F1 B:W5Q401 0.0 20.0 0.6 C9 B:W5Q401 1.4 20.0 0.6 C8 B:W5Q401 2.3 20.0 0.6 C10 B:W5Q401 2.3 20.0 0.6 HZ B:PHE96 2.5 51.9 1.0 HA B:THR7 3.2 48.0 1.0 CZ B:PHE96 3.3 43.2 1.0 HD12 B:ILE92 3.6 61.0 1.0 C11 B:W5Q401 3.6 20.0 0.6 C7 B:W5Q401 3.6 20.0 0.6 HE2 B:PHE96 3.8 53.5 1.0 HG23 B:THR7 3.9 76.0 1.0 O B:THR7 4.0 44.1 1.0 CE2 B:PHE96 4.0 44.6 1.0 C6 B:W5Q401 4.1 20.0 0.6 HG1 B:THR7 4.1 50.1 1.0 CA B:THR7 4.1 40.0 1.0 HD1 B:HIS31 4.2 49.9 1.0 CE1 B:PHE96 4.3 55.0 1.0 HE1 B:PHE96 4.3 66.0 1.0 HG23 B:ILE92 4.4 64.0 1.0 CD1 B:ILE92 4.4 50.8 1.0 HD11 B:ILE92 4.5 61.0 1.0 HG21 B:ILE92 4.6 64.0 1.0 C B:THR7 4.6 36.4 1.0 F B:W5Q401 4.7 20.0 0.6 O B:PHE6 4.7 36.0 1.0 CG2 B:THR7 4.7 63.4 1.0 HE1 B:HIS31 4.8 65.9 1.0 OG1 B:THR7 4.8 41.7 1.0 CB B:THR7 4.8 38.5 1.0 ND1 B:HIS31 4.8 41.6 1.0 HD13 B:ILE92 4.8 61.0 1.0 CG2 B:ILE92 5.0 53.3 1.0

Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 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 P08B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.60 F B:W5Q401 0.0 20.0 0.6 C11 B:W5Q401 1.3 20.0 0.6 C10 B:W5Q401 2.3 20.0 0.6 C6 B:W5Q401 2.3 20.0 0.6 HB2 B:PRO5 2.6 37.7 1.0 C4 B:W5Q401 2.8 20.0 0.6 HB2 B:TYR68 2.9 40.4 1.0 C5 B:W5Q401 3.0 20.0 0.6 HG2 B:PRO5 3.1 45.9 1.0 HD2 B:TYR68 3.2 45.1 1.0 CB B:PRO5 3.5 31.4 1.0 CB B:TYR68 3.5 33.7 1.0 CD2 B:TYR68 3.5 37.6 1.0 HB3 B:TYR68 3.5 40.4 1.0 HG21 B:ILE92 3.5 64.0 1.0 C9 B:W5Q401 3.6 20.0 0.6 C7 B:W5Q401 3.6 20.0 0.6 CG B:TYR68 3.6 32.0 1.0 CG B:PRO5 3.7 38.2 1.0 HG1 B:THR7 3.8 50.1 1.0 HE2 B:PHE96 4.0 53.5 1.0 C B:PRO5 4.0 29.3 1.0 OG1 B:THR7 4.1 41.7 1.0 O B:PRO5 4.1 33.3 1.0 C8 B:W5Q401 4.1 20.0 0.6 HA B:THR7 4.1 48.0 1.0 HB3 B:PRO5 4.1 37.7 1.0 HG3 B:PRO5 4.2 45.9 1.0 CA B:PRO5 4.3 30.6 1.0 N1 B:W5Q401 4.3 20.0 0.6 CE2 B:TYR68 4.3 37.7 1.0 N B:THR7 4.4 37.7 1.0 N B:PHE6 4.4 30.4 1.0 CG2 B:ILE92 4.4 53.3 1.0 C B:PHE6 4.4 36.2 1.0 H B:PHE6 4.6 36.4 1.0 CD1 B:TYR68 4.6 35.9 1.0 HG22 B:ILE92 4.6 64.0 1.0 H B:THR7 4.6 45.2 1.0 HE2 B:TYR68 4.6 45.2 1.0 CA B:THR7 4.7 40.0 1.0 F1 B:W5Q401 4.7 20.0 0.6 HA B:PHE6 4.7 36.9 1.0 O B:PHE6 4.8 36.0 1.0 HG23 B:ILE92 4.8 64.0 1.0 H B:ILE69 4.8 35.0 1.0 CA B:PHE6 4.8 30.8 1.0 CE2 B:PHE96 4.9 44.6 1.0 CA B:TYR68 4.9 30.4 1.0 CD B:PRO5 4.9 33.4 1.0 HE1 B:PHE89 4.9 46.4 1.0 HD1 B:TYR68 5.0 43.0 1.0

Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 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 P08B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.52 F1 B:WKH402 0.0 20.0 0.5 C9 B:WKH402 1.3 20.0 0.5 C10 B:WKH402 2.2 20.0 0.5 C8 B:WKH402 2.3 20.0 0.5 HD3 B:PRO106 2.7 50.3 1.0 HG21 B:ILE17 3.2 43.6 1.0 HA B:TYR105 3.3 36.5 1.0 HG21 B:VAL103 3.4 45.3 1.0 HG23 B:VAL103 3.4 45.3 1.0 C11 B:WKH402 3.5 20.0 0.5 C7 B:WKH402 3.6 20.0 0.5 HG23 B:ILE33 3.7 36.0 1.0 CD B:PRO106 3.7 41.9 1.0 HE2 B:PHE22 3.8 45.9 1.0 O B:SER104 3.8 36.0 1.0 HG3 B:PRO106 3.8 58.6 1.0 CG2 B:VAL103 3.8 37.8 1.0 HB B:VAL103 3.8 47.4 1.0 HD2 B:PHE22 3.9 45.3 1.0 HG22 B:ILE17 3.9 43.6 1.0 CG2 B:ILE17 3.9 36.4 1.0 CE2 B:PHE22 4.0 38.3 1.0 C6 B:WKH402 4.0 20.0 0.5 CD2 B:PHE22 4.0 37.8 1.0 HD2 B:PRO106 4.2 50.3 1.0 HG21 B:ILE33 4.2 36.0 1.0 CA B:TYR105 4.2 30.4 1.0 CG B:PRO106 4.3 48.8 1.0 C B:SER104 4.3 35.4 1.0 HD13 B:ILE33 4.4 37.9 1.0 CG2 B:ILE33 4.4 30.0 1.0 HG23 B:ILE17 4.4 43.6 1.0 CB B:VAL103 4.4 39.5 1.0 N B:PRO106 4.4 38.3 1.0 HG12 B:ILE33 4.5 36.8 1.0 N B:TYR105 4.5 33.8 1.0 F B:WKH402 4.5 20.0 0.5 HB2 B:TYR20 4.6 45.2 1.0 HB3 B:PRO106 4.7 64.2 1.0 HG22 B:VAL103 4.7 45.3 1.0 CZ B:PHE22 4.8 44.3 1.0 C B:TYR105 4.8 35.7 1.0 HB3 B:TYR20 4.8 45.2 1.0 CG B:PHE22 4.9 37.6 1.0 HB3 B:PHE22 5.0 48.6 1.0 HB B:ILE17 5.0 38.4 1.0 HG22 B:ILE33 5.0 36.0 1.0

Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B02 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 P08B02 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.52 F B:WKH402 0.0 20.0 0.5 C11 B:WKH402 1.3 20.0 0.5 C6 B:WKH402 2.3 20.0 0.5 C10 B:WKH402 2.3 20.0 0.5 C4 B:WKH402 2.6 20.0 0.5 C9 B:WKH402 3.5 20.0 0.5 C7 B:WKH402 3.5 20.0 0.5 N1 B:WKH402 3.6 20.0 0.5 C5 B:WKH402 3.7 20.0 0.5 HB3 B:PRO106 4.0 64.2 1.0 C8 B:WKH402 4.0 20.0 0.5 HB B:VAL103 4.2 47.4 1.0 HG3 B:PRO106 4.2 58.6 1.0 HB3 B:PHE22 4.3 48.6 1.0 F1 B:WKH402 4.5 20.0 0.5 HG11 B:VAL103 4.8 52.0 1.0 CB B:PRO106 4.8 53.5 1.0 C3 B:WKH402 4.9 20.0 0.5 HG12 B:VAL103 4.9 52.0 1.0 CG B:PRO106 4.9 48.8 1.0 O B:SER104 5.0 36.0 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