Fluorine in PDB 5rbv: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A:
3.4.23.22;

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A, PDB code: 5rbv was solved by M.S.Weiss, J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.48 / 0.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.231, 72.966, 52.337, 90.00, 109.17, 90.00
R / Rfree (%)	16.6 / 16.7

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A (pdb code 5rbv). 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 -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A, PDB code: 5rbv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A


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 -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:15.8 occ:0.23 F A:RQD401 0.0 15.9 0.1 F A:RQD401 0.0 15.8 0.2 C7 A:RQD401 1.4 14.5 0.2 C7 A:RQD401 1.4 14.9 0.1 O A:HOH743 1.5 34.5 0.3 O A:HOH743 1.8 51.2 0.3 C8 A:RQD401 2.3 14.3 0.2 C8 A:RQD401 2.3 14.6 0.1 C6 A:RQD401 2.3 15.0 0.1 C6 A:RQD401 2.3 14.6 0.2 OG A:SER83 2.9 18.1 0.3 OG A:SER83 2.9 18.1 0.3 OG A:SER83 2.9 13.7 0.2 CZ A:PHE116 2.9 13.5 0.3 CZ A:PHE116 2.9 13.5 0.3 OG A:SER83 3.0 15.3 0.1 CE1 A:PHE116 3.3 13.5 0.3 CE1 A:PHE116 3.3 13.5 0.3 CZ A:PHE116 3.4 12.0 0.1 CZ A:PHE116 3.4 11.4 0.2 C9 A:RQD401 3.6 13.6 0.2 C9 A:RQD401 3.6 14.1 0.1 OD2 A:ASP81 3.6 17.8 0.2 C5 A:RQD401 3.6 14.2 0.2 C5 A:RQD401 3.6 14.5 0.1 OD2 A:ASP81 3.7 26.9 0.3 OD2 A:ASP81 3.7 26.7 0.3 OD1 A:ASP81 3.7 16.3 0.1 CE1 A:PHE116 3.7 11.6 0.1 OD1 A:ASP81 3.8 16.4 0.2 CB A:SER83 3.8 16.2 0.3 CB A:SER83 3.8 16.1 0.3 CE1 A:PHE116 3.8 10.8 0.2 CE2 A:PHE116 3.8 13.3 0.3 CE2 A:PHE116 3.8 13.3 0.3 CD1 A:TYR79 3.9 11.4 0.2 CB A:TYR79 3.9 13.4 0.1 OD1 A:ASP81 4.0 22.5 0.3 OD1 A:ASP81 4.0 22.5 0.3 CB A:TYR79 4.0 11.8 0.2 CG A:TYR79 4.0 13.1 0.1 CG A:ASP81 4.0 16.0 0.2 CD1 A:TYR79 4.0 13.0 0.1 CG A:TYR79 4.0 11.4 0.2 C4 A:RQD401 4.1 13.4 0.2 C4 A:RQD401 4.1 13.9 0.1 CB A:SER83 4.1 14.2 0.2 CB A:SER83 4.1 15.6 0.1 CD1 A:TYR79 4.1 12.8 0.3 CD1 A:TYR79 4.1 12.8 0.3 CG A:ASP81 4.2 23.1 0.3 CG A:ASP81 4.2 23.0 0.3 OD2 A:ASP81 4.2 16.8 0.1 CG A:ASP81 4.2 16.0 0.1 CE2 A:PHE116 4.3 11.1 0.2 CE2 A:PHE116 4.3 11.8 0.1 CD1 A:PHE116 4.4 12.5 0.3 CD1 A:PHE116 4.4 12.6 0.3 CG A:TYR79 4.4 14.0 0.3 CG A:TYR79 4.4 14.0 0.3 CB A:TYR79 4.6 15.3 0.3 CB A:TYR79 4.6 15.3 0.3 CE1 A:TYR79 4.6 11.2 0.2 CE1 A:TYR79 4.7 12.3 0.3 CE1 A:TYR79 4.7 12.2 0.3 CD2 A:TYR79 4.7 13.1 0.1 CE1 A:TYR79 4.8 12.8 0.1 CD2 A:PHE116 4.8 12.9 0.3 CD2 A:PHE116 4.8 12.9 0.3 CD1 A:PHE116 4.8 11.8 0.1 O A:HOH694 4.8 28.1 0.3 CD1 A:PHE116 4.9 11.0 0.2 CD2 A:TYR79 4.9 11.4 0.2 C1 A:DMS402 5.0 27.0 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A


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 -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D04A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:15.9 occ:0.12 F A:RQD401 0.0 15.9 0.1 F A:RQD401 0.0 15.8 0.2 C7 A:RQD401 1.4 14.5 0.2 C7 A:RQD401 1.4 14.9 0.1 O A:HOH743 1.5 34.5 0.3 O A:HOH743 1.8 51.2 0.3 C8 A:RQD401 2.3 14.3 0.2 C8 A:RQD401 2.3 14.6 0.1 C6 A:RQD401 2.3 15.0 0.1 C6 A:RQD401 2.3 14.6 0.2 OG A:SER83 2.9 18.1 0.3 OG A:SER83 2.9 18.1 0.3 OG A:SER83 2.9 13.7 0.2 CZ A:PHE116 2.9 13.5 0.3 CZ A:PHE116 2.9 13.5 0.3 OG A:SER83 3.0 15.3 0.1 CE1 A:PHE116 3.3 13.5 0.3 CE1 A:PHE116 3.3 13.5 0.3 CZ A:PHE116 3.4 12.0 0.1 CZ A:PHE116 3.4 11.4 0.2 C9 A:RQD401 3.6 13.6 0.2 C9 A:RQD401 3.6 14.1 0.1 OD2 A:ASP81 3.6 17.8 0.2 C5 A:RQD401 3.6 14.2 0.2 C5 A:RQD401 3.6 14.5 0.1 OD2 A:ASP81 3.7 26.9 0.3 OD2 A:ASP81 3.7 26.7 0.3 OD1 A:ASP81 3.7 16.3 0.1 CE1 A:PHE116 3.7 11.6 0.1 OD1 A:ASP81 3.8 16.4 0.2 CB A:SER83 3.8 16.2 0.3 CB A:SER83 3.8 16.1 0.3 CE1 A:PHE116 3.8 10.8 0.2 CE2 A:PHE116 3.8 13.3 0.3 CE2 A:PHE116 3.8 13.3 0.3 CD1 A:TYR79 3.9 11.4 0.2 CB A:TYR79 3.9 13.4 0.1 OD1 A:ASP81 4.0 22.5 0.3 OD1 A:ASP81 4.0 22.5 0.3 CB A:TYR79 4.0 11.8 0.2 CG A:TYR79 4.0 13.1 0.1 CG A:ASP81 4.0 16.0 0.2 CD1 A:TYR79 4.0 13.0 0.1 CG A:TYR79 4.0 11.4 0.2 C4 A:RQD401 4.1 13.4 0.2 C4 A:RQD401 4.1 13.9 0.1 CB A:SER83 4.1 14.2 0.2 CB A:SER83 4.1 15.6 0.1 CD1 A:TYR79 4.1 12.8 0.3 CD1 A:TYR79 4.1 12.8 0.3 CG A:ASP81 4.2 23.1 0.3 CG A:ASP81 4.2 23.0 0.3 OD2 A:ASP81 4.2 16.8 0.1 CG A:ASP81 4.2 16.0 0.1 CE2 A:PHE116 4.3 11.1 0.2 CE2 A:PHE116 4.3 11.8 0.1 CD1 A:PHE116 4.4 12.5 0.3 CD1 A:PHE116 4.4 12.6 0.3 CG A:TYR79 4.4 14.0 0.3 CG A:TYR79 4.4 14.0 0.3 CB A:TYR79 4.6 15.3 0.3 CB A:TYR79 4.6 15.3 0.3 CE1 A:TYR79 4.6 11.2 0.2 CE1 A:TYR79 4.7 12.3 0.3 CE1 A:TYR79 4.7 12.2 0.3 CD2 A:TYR79 4.7 13.1 0.1 CE1 A:TYR79 4.8 12.8 0.1 CD2 A:PHE116 4.8 12.9 0.3 CD2 A:PHE116 4.8 12.9 0.3 CD1 A:PHE116 4.8 11.8 0.1 O A:HOH694 4.8 28.1 0.3 CD1 A:PHE116 4.9 11.0 0.2 CD2 A:TYR79 4.9 11.4 0.2 C1 A:DMS402 5.0 27.0 1.0

J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, M.S.Weiss. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries For Crystallographic Fragment Screening. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32413289
DOI: 10.1016/J.STR.2020.04.019