Fluorine in PDB 5sub: Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 From the F2X-Universal Library

The structure of Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 From the F2X-Universal Library, PDB code: 5sub 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)	37.00 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.627, 82.049, 94.132, 90, 108.42, 90
R / Rfree (%)	20.7 / 23.5

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 From the F2X-Universal Library (pdb code 5sub). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 From the F2X-Universal Library, PDB code: 5sub:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 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 P03G01 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ A:F2101 b:20.0 occ:0.38 F A:V6R2101 0.0 20.0 0.4 C11 A:V6R2101 1.3 20.0 0.4 C10 A:V6R2101 2.3 20.0 0.4 C6 A:V6R2101 2.3 20.0 0.4 C5 A:V6R2101 2.8 20.0 0.4 HB2 A:ASN1990 3.1 44.6 1.0 O A:V6R2101 3.1 20.0 0.4 N A:V6R2101 3.1 20.0 0.4 HA A:HIS1888 3.2 37.2 1.0 C3 A:V6R2101 3.2 20.0 0.4 O A:PHE1989 3.3 32.5 1.0 C A:PHE1989 3.4 34.5 1.0 HA A:ASN1990 3.4 42.8 1.0 N A:ASN1990 3.4 32.2 1.0 HD2 A:HIS1888 3.5 47.5 1.0 C9 A:V6R2101 3.5 20.0 0.4 C7 A:V6R2101 3.6 20.0 0.4 CA A:ASN1990 3.7 35.7 1.0 CD2 A:HIS1888 3.7 39.6 1.0 C4 A:V6R2101 3.7 20.0 0.4 H A:ASN1990 3.8 38.6 1.0 H A:LEU1889 3.8 37.3 1.0 CB A:ASN1990 3.8 37.2 1.0 HB3 A:LEU1988 3.8 47.8 1.0 C8 A:V6R2101 4.0 20.0 0.4 N1 A:V6R2101 4.1 20.0 0.4 CG A:HIS1888 4.1 37.0 1.0 CA A:HIS1888 4.2 31.0 1.0 N A:PHE1989 4.2 35.4 1.0 CA A:PHE1989 4.2 33.9 1.0 H A:PHE1989 4.2 42.5 1.0 NE2 A:HIS1888 4.3 42.0 1.0 HA A:PHE1989 4.3 40.6 1.0 C2 A:V6R2101 4.3 20.0 0.4 HB3 A:ASN1990 4.5 44.6 1.0 HB3 A:HIS1888 4.5 41.5 1.0 CB A:HIS1888 4.5 34.6 1.0 HE2 A:HIS1888 4.5 50.4 1.0 N A:LEU1889 4.6 31.1 1.0 C A:LEU1988 4.6 36.0 1.0 HD22 A:ASN1990 4.7 55.1 1.0 CB A:LEU1988 4.8 39.9 1.0 CG A:ASN1990 4.8 36.7 1.0 ND1 A:HIS1888 4.9 48.2 1.0 C A:HIS1888 4.9 35.4 1.0 CE1 A:HIS1888 4.9 47.0 1.0

Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 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 P03G01 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:20.0 occ:0.42 F B:V6R401 0.0 20.0 0.4 C11 B:V6R401 1.3 20.0 0.4 HE21 B:GLN28 2.2 91.3 1.0 C6 B:V6R401 2.3 20.0 0.4 C10 B:V6R401 2.3 20.0 0.4 C5 B:V6R401 2.7 20.0 0.4 HE22 B:GLN28 2.7 91.3 1.0 NE2 B:GLN28 2.8 76.1 1.0 O B:V6R401 3.1 20.0 0.4 N B:V6R401 3.3 20.0 0.4 C3 B:V6R401 3.4 20.0 0.4 O B:PRO29 3.5 60.1 1.0 C7 B:V6R401 3.5 20.0 0.4 C9 B:V6R401 3.5 20.0 0.4 HD1 B:PHE30 3.7 58.0 1.0 C8 B:V6R401 4.0 20.0 0.4 CD B:GLN28 4.0 61.6 1.0 C B:V6R401 4.1 20.0 0.4 HG2 B:GLN28 4.2 69.7 1.0 HA B:PHE30 4.2 51.5 1.0 HB2 B:PHE30 4.3 50.8 1.0 HG13 B:VAL103 4.4 55.4 1.0 C B:PRO29 4.6 58.6 1.0 CD1 B:PHE30 4.7 48.4 1.0 CG B:GLN28 4.7 58.1 1.0 C4 B:V6R401 4.7 20.0 0.4 C2 B:V6R401 4.7 20.0 0.4 HG12 B:VAL103 4.8 55.4 1.0 C1 B:V6R401 4.9 20.0 0.4 CA B:PHE30 4.9 42.9 1.0 CG1 B:VAL103 4.9 46.1 1.0 HB2 B:PRO29 5.0 75.1 1.0 OE1 B:GLN28 5.0 54.7 1.0 CB B:PHE30 5.0 42.3 1.0

Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- AAR2/Rnaseh in Complex with Fragment P03G01 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 P03G01 From the F2X-Universal Library within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:20.0 occ:0.42 F B:V6R402 0.0 20.0 0.4 C11 B:V6R402 1.3 20.0 0.4 C10 B:V6R402 2.3 20.0 0.4 C6 B:V6R402 2.3 20.0 0.4 C5 B:V6R402 2.8 20.0 0.4 C9 B:V6R402 3.5 20.0 0.4 C7 B:V6R402 3.5 20.0 0.4 N B:V6R402 3.8 20.0 0.4 C4 B:V6R402 3.8 20.0 0.4 HB3 B:PHE22 3.9 49.6 1.0 C4 B:V6R401 3.9 20.0 0.4 HB2 B:PHE22 3.9 49.6 1.0 C8 B:V6R402 4.0 20.0 0.4 CB B:PHE22 4.4 41.3 1.0 HG12 B:VAL103 4.5 55.4 1.0 HB B:VAL103 4.6 48.3 1.0 C1 B:V6R401 4.6 20.0 0.4 HG11 B:VAL103 4.9 55.4 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