Fluorine in PDB 7foi: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 From the F2X-Universal Library, PDB code: 7foi 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)	44.76 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.759, 82.149, 93.693, 90, 108.29, 90
R / Rfree (%)	21.1 / 24.9

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 From the F2X-Universal Library (pdb code 7foi). 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 P08B06 From the F2X-Universal Library, PDB code: 7foi:
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 P08B06 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 P08B06 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.40 F B:W5Z401 0.0 20.0 0.4 C4 B:W5Z401 1.3 20.0 0.4 C3 B:W5Z401 2.3 20.0 0.4 C5 B:W5Z401 2.3 20.0 0.4 HB2 B:PRO5 2.4 53.1 1.0 HG2 B:PRO5 2.5 56.0 1.0 HG21 B:ILE92 2.9 74.1 1.0 HB2 B:TYR68 2.9 48.5 1.0 CB B:PRO5 3.1 44.2 1.0 CG B:PRO5 3.2 46.6 1.0 HE2 B:PHE96 3.3 62.0 1.0 HB3 B:TYR68 3.4 48.5 1.0 HG22 B:ILE92 3.4 74.1 1.0 HG3 B:PRO5 3.4 56.0 1.0 C2 B:W5Z401 3.5 20.0 0.4 C B:W5Z401 3.5 20.0 0.4 CB B:TYR68 3.5 40.4 1.0 CG2 B:ILE92 3.6 61.8 1.0 C8 B:W5Z401 3.6 20.0 0.4 HB3 B:PRO5 3.8 53.1 1.0 CG B:TYR68 4.0 43.5 1.0 C1 B:W5Z401 4.0 20.0 0.4 CA B:PRO5 4.1 39.6 1.0 C B:PRO5 4.1 35.3 1.0 CE2 B:PHE96 4.2 51.7 1.0 HG23 B:ILE92 4.2 74.1 1.0 HD2 B:TYR68 4.2 54.7 1.0 C7 B:W5Z401 4.3 20.0 0.4 CD2 B:TYR68 4.3 45.6 1.0 O B:PRO5 4.3 40.5 1.0 HE1 B:PHE89 4.4 51.9 1.0 CD B:PRO5 4.5 41.7 1.0 HD1 B:PHE89 4.5 62.9 1.0 N B:PHE6 4.5 37.3 1.0 HB B:ILE92 4.6 68.9 1.0 HG13 B:ILE92 4.6 69.8 1.0 N1 B:W5Z401 4.6 20.0 0.4 CD1 B:TYR68 4.7 45.3 1.0 CB B:ILE92 4.7 57.4 1.0 HD2 B:PRO5 4.7 50.1 1.0 C6 B:W5Z401 4.7 20.0 0.4 HD2 B:PHE96 4.7 74.0 1.0 H B:PHE6 4.7 44.8 1.0 O B:PHE6 4.8 42.4 1.0 HA B:PRO5 4.8 47.5 1.0 HA B:THR7 4.8 59.3 1.0 C B:PHE6 4.8 43.2 1.0 HA B:TYR68 4.8 46.4 1.0 HD1 B:TYR68 4.9 54.4 1.0 CA B:TYR68 4.9 38.7 1.0 HG22 B:VAL93 4.9 73.8 1.0 HZ B:PHE96 4.9 62.2 1.0 N B:W5Z401 4.9 20.0 0.4 CD2 B:PHE96 4.9 61.7 1.0 CE1 B:PHE89 4.9 43.3 1.0 N B:PRO5 4.9 40.5 1.0 CD1 B:PHE89 5.0 52.5 1.0 CZ B:PHE96 5.0 51.8 1.0

Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 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 P08B06 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.56 F B:W5Z402 0.0 20.0 0.6 C4 B:W5Z402 1.3 20.0 0.6 C5 B:W5Z402 2.3 20.0 0.6 C3 B:W5Z402 2.3 20.0 0.6 C B:W5Z402 3.5 20.0 0.6 C2 B:W5Z402 3.5 20.0 0.6 O B:GLN100 3.7 48.0 1.0 HE2 B:MET101 4.0 96.4 1.0 C1 B:W5Z402 4.0 20.0 0.6 HE1 B:MET101 4.2 96.4 1.0 CE B:MET101 4.5 80.4 1.0 HB2 B:GLN100 4.6 62.9 1.0 C6 B:W5Z402 4.7 20.0 0.6 N B:W5Z402 4.7 20.0 0.6 HB3 B:GLN100 4.7 62.9 1.0 C B:GLN100 4.8 46.4 1.0 HA B:MET101 4.9 57.5 1.0 SD B:MET101 4.9 104.7 1.0

Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 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 P08B06 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:20.0 occ:0.50 F B:W5Z403 0.0 20.0 0.5 C4 B:W5Z403 1.3 20.0 0.5 C3 B:W5Z403 2.3 20.0 0.5 C5 B:W5Z403 2.3 20.0 0.5 HB2 B:SER240 2.6 49.8 1.0 HA B:TYR237 3.0 50.3 1.0 HD23 B:LEU283 3.0 80.8 1.0 HG B:SER240 3.1 56.2 1.0 CB B:SER240 3.3 41.5 1.0 HB3 B:SER240 3.3 49.8 1.0 HD22 B:LEU283 3.4 80.8 1.0 C2 B:W5Z403 3.5 20.0 0.5 C B:W5Z403 3.5 20.0 0.5 CD2 B:LEU283 3.6 67.3 1.0 OG B:SER240 3.6 46.9 1.0 HG23 B:ILE282 3.7 91.7 1.0 HO1 B:PGR405 3.7 20.0 1.0 HD1 B:TYR237 3.8 74.3 1.0 HA2 B:GLY235 3.8 54.2 1.0 O B:ASN236 3.8 42.0 1.0 HD21 B:LEU283 3.8 80.8 1.0 CA B:TYR237 3.9 42.0 1.0 HA B:LEU283 4.0 64.3 1.0 C1 B:W5Z403 4.0 20.0 0.5 N B:TYR237 4.1 39.4 1.0 C B:ASN236 4.1 52.6 1.0 HB1 B:ALA231 4.1 46.8 1.0 O1 B:PGR405 4.1 20.0 1.0 H B:SER240 4.3 46.5 1.0 C B:GLY235 4.3 46.4 1.0 H B:TYR237 4.4 47.2 1.0 O B:ILE282 4.5 64.7 1.0 HA B:ALA231 4.5 47.5 1.0 CG2 B:ILE282 4.5 76.4 1.0 CA B:GLY235 4.5 45.2 1.0 O B:GLY235 4.5 47.7 1.0 N B:ASN236 4.5 42.3 1.0 O B:HOH506 4.5 30.0 1.0 CA B:SER240 4.6 40.3 1.0 HG21 B:ILE282 4.6 91.7 1.0 CD1 B:TYR237 4.7 62.0 1.0 H33 B:PGR405 4.7 20.0 1.0 C6 B:W5Z403 4.7 20.0 0.5 O B:ALA231 4.7 41.7 1.0 HG22 B:ILE282 4.7 91.7 1.0 H B:ASN236 4.7 50.8 1.0 HB2 B:TYR237 4.7 54.5 1.0 O B:TYR237 4.7 41.5 1.0 C B:TYR237 4.8 39.1 1.0 CB B:TYR237 4.9 45.5 1.0 CB B:ALA231 4.9 39.0 1.0 N B:SER240 4.9 38.7 1.0 H2 B:PGR405 4.9 20.0 1.0 CA B:LEU283 4.9 53.6 1.0 HA3 B:GLY235 4.9 54.2 1.0 HA B:SER240 4.9 48.3 1.0

Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P08B06 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 P08B06 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:20.0 occ:0.34 F B:W5Z404 0.0 20.0 0.3 C4 B:W5Z404 1.3 20.0 0.3 C5 B:W5Z404 2.3 20.0 0.3 C3 B:W5Z404 2.3 20.0 0.3 HA3 B:GLY222 2.5 52.0 1.0 H B:GLN122 2.6 57.8 0.6 H B:GLN122 2.6 57.8 0.4 HA B:VAL121 2.6 51.1 1.0 O B:PHE120 3.1 42.9 1.0 CA B:GLY222 3.2 43.4 1.0 C B:GLY222 3.2 39.7 1.0 N B:GLN122 3.4 48.2 0.4 N B:GLN122 3.4 48.1 0.6 HA2 B:GLY222 3.5 52.0 1.0 CA B:VAL121 3.5 42.6 1.0 O B:GLY222 3.5 35.9 1.0 C B:W5Z404 3.5 20.0 0.3 C2 B:W5Z404 3.5 20.0 0.3 HG3 B:GLN122 3.6 71.8 0.6 HB2 B:LYS125 3.6 55.0 1.0 HG2 B:GLN122 3.7 68.8 0.4 N B:GLU223 3.7 39.7 1.0 HG13 B:VAL121 3.7 47.3 1.0 C B:VAL121 3.9 47.4 1.0 HB2 B:GLN122 3.9 66.5 0.4 HB2 B:GLN122 3.9 66.1 0.6 C1 B:W5Z404 4.0 20.0 0.3 H B:GLU223 4.0 47.7 1.0 C B:PHE120 4.0 40.3 1.0 HB3 B:LYS125 4.1 55.0 1.0 HG3 B:LYS125 4.1 69.0 1.0 HA B:GLU223 4.2 50.9 1.0 N B:VAL121 4.2 37.6 1.0 CB B:LYS125 4.2 45.9 1.0 HG22 B:VAL121 4.3 44.9 1.0 CG B:GLN122 4.4 59.8 0.6 HA B:ASN219 4.4 57.1 1.0 CB B:GLN122 4.4 55.1 0.6 CB B:GLN122 4.4 55.5 0.4 N B:GLY222 4.4 37.2 1.0 CA B:GLN122 4.4 51.0 0.6 CA B:GLN122 4.5 51.0 0.4 CG1 B:VAL121 4.5 39.4 1.0 CB B:VAL121 4.5 39.3 1.0 HB2 B:PHE226 4.5 42.9 1.0 CG B:GLN122 4.5 57.3 0.4 O B:ASN219 4.5 41.9 1.0 H B:GLY222 4.5 44.6 1.0 CA B:GLU223 4.5 42.4 1.0 O B:GLN122 4.6 47.1 0.4 O B:GLN122 4.6 46.8 0.6 HG13 B:ILE126 4.7 56.9 1.0 HB2 B:GLU223 4.7 52.4 1.0 HG12 B:VAL121 4.7 47.3 1.0 CG B:LYS125 4.7 57.5 1.0 C6 B:W5Z404 4.7 20.0 0.3 CG2 B:VAL121 4.9 37.4 1.0 HG3 B:GLN122 4.9 68.8 0.4 OE1 B:GLN122 5.0 56.4 0.6 CD B:GLN122 5.0 59.2 0.6

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