Fluorine in PDB 5r1x: Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free:
3.4.23.22;

The structure of Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free, PDB code: 5r1x was solved by J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.52 / 1.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.284, 72.919, 52.701, 90.00, 109.34, 90.00
R / Rfree (%)	11.4 / 12.7

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free (pdb code 5r1x). 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 in Complex with Fragment F2X-Entry D04, Dmso-Free, PDB code: 5r1x:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free


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 in Complex with Fragment F2X-Entry D04, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.0 occ:1.00 F A:RQD401 0.0 30.0 1.0 C7 A:RQD401 1.3 30.0 1.0 C8 A:RQD401 2.3 30.0 1.0 C6 A:RQD401 2.3 30.0 1.0 H A:RQD402 2.4 30.0 1.0 HE1 A:PHE116 2.5 19.7 1.0 H11 A:RQD401 2.6 30.0 1.0 H10 A:RQD401 2.6 30.0 1.0 O A:HOH507 3.1 46.7 1.0 O A:HOH793 3.1 25.3 1.0 C1 A:RQD402 3.1 30.0 1.0 C2 A:RQD402 3.1 30.0 1.0 CE1 A:PHE116 3.2 16.4 1.0 O1 A:RQD402 3.4 30.0 1.0 H2 A:RQD402 3.5 30.0 1.0 O A:HOH516 3.5 44.8 1.0 C9 A:RQD401 3.6 30.0 1.0 C5 A:RQD401 3.6 30.0 1.0 O A:RQD402 3.6 30.0 1.0 HD11 A:LEU125 3.8 16.9 1.0 HD1 A:PHE116 3.8 19.5 1.0 N A:RQD402 3.8 30.0 1.0 CD1 A:PHE116 3.9 16.2 1.0 CZ A:PHE116 3.9 16.9 1.0 HD13 A:ILE122 3.9 17.7 1.0 HZ A:PHE116 3.9 20.4 1.0 C4 A:RQD401 4.1 30.0 1.0 HD12 A:ILE122 4.2 17.7 1.0 HG21 A:ILE122 4.2 14.2 1.0 C3 A:RQD402 4.4 30.0 1.0 H12 A:RQD401 4.4 30.0 1.0 H9 A:RQD401 4.5 30.0 1.0 H5 A:RQD402 4.5 30.0 1.0 CD1 A:ILE122 4.5 14.7 1.0 H1 A:RQD402 4.5 30.0 1.0 H8 A:RQD402 4.5 30.0 1.0 H3 A:RQD402 4.5 30.0 1.0 C A:RQD402 4.6 30.0 1.0 CD1 A:LEU125 4.7 14.1 1.0 H7 A:RQD402 4.8 30.0 1.0 HD21 A:LEU125 4.8 19.6 1.0 HD13 A:LEU125 4.9 16.9 1.0 HD12 A:LEU125 4.9 16.9 1.0 HD11 A:ILE122 5.0 17.7 1.0 OD2 A:ASP33 5.0 12.6 1.0

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin in Complex with Fragment F2X-Entry D04, Dmso-Free


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 in Complex with Fragment F2X-Entry D04, Dmso-Free within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:30.0 occ:1.00 F A:RQD402 0.0 30.0 1.0 C7 A:RQD402 1.4 30.0 1.0 C6 A:RQD402 2.3 30.0 1.0 C8 A:RQD402 2.3 30.0 1.0 H10 A:RQD402 2.6 30.0 1.0 H11 A:RQD402 2.6 30.0 1.0 CG A:ASP15 3.3 16.4 1.0 OD2 A:ASP15 3.3 16.1 1.0 OD1 A:ASP15 3.4 18.1 1.0 C5 A:RQD402 3.6 30.0 1.0 C9 A:RQD402 3.6 30.0 1.0 HB3 A:ASP15 3.7 17.4 1.0 CB A:ASP15 4.1 14.5 1.0 C4 A:RQD402 4.1 30.0 1.0 H12 A:RQD402 4.4 30.0 1.0 H9 A:RQD402 4.5 30.0 1.0 HB2 A:ASP15 4.5 17.4 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