Fluorine in PDB 7hgn: Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006, PDB code: 7hgn was solved by T.Vantieghem, E.Osipov, D.Fearon, A.Douangamath, F.Von Delft, S.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.55 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.31, 41.92, 158.03, 90, 90, 90
R / Rfree (%)	20 / 24.3

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 (pdb code 7hgn). 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 -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006, PDB code: 7hgn:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006


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 -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ B:F103 b:37.7 occ:0.84 F B:NX7103 0.0 37.7 0.8 C B:NX7103 1.3 35.8 0.8 C5 B:NX7103 2.3 31.0 0.8 C1 B:NX7103 2.4 40.3 0.8 C6 B:NX7103 2.8 28.9 0.8 CB B:GLU49 3.2 39.5 1.0 CD1 B:PHE44 3.3 26.3 1.0 N B:NX7103 3.3 27.9 0.8 CE1 B:PHE44 3.3 33.5 1.0 C10 B:NX7103 3.5 27.8 0.8 O B:NX7103 3.5 34.1 0.8 C4 B:NX7103 3.6 37.6 0.8 C2 B:NX7103 3.6 39.1 0.8 O B:THR50 3.9 33.8 1.0 N B:THR50 4.1 31.9 1.0 C3 B:NX7103 4.1 37.1 0.8 CG B:PHE44 4.1 22.4 1.0 C B:THR50 4.1 34.8 1.0 C B:GLU49 4.1 32.9 1.0 CG B:GLU49 4.2 41.9 1.0 CZ B:PHE44 4.2 28.5 1.0 C9 B:NX7103 4.3 27.0 0.8 C7 B:NX7103 4.4 28.7 0.8 CE B:MET15 4.4 51.0 1.0 CB B:ALA51 4.4 34.1 1.0 CA B:GLU49 4.4 32.9 1.0 SD B:MET15 4.4 40.8 1.0 OE1 B:GLU49 4.6 50.4 1.0 CA B:THR50 4.6 33.3 1.0 O B:GLU49 4.6 32.2 1.0 F1 B:NX7103 4.7 37.1 0.8 CD B:GLU49 4.7 46.4 1.0 N B:ALA51 4.7 33.0 1.0 CB B:PHE44 4.8 22.2 1.0 CD2 B:PHE44 4.8 22.6 1.0 CE2 B:PHE44 4.8 29.1 1.0

Fluorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006


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 -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ B:F103 b:37.1 occ:0.84 F1 B:NX7103 0.0 37.1 0.8 C4 B:NX7103 1.4 37.6 0.8 C5 B:NX7103 2.3 31.0 0.8 C3 B:NX7103 2.4 37.1 0.8 C6 B:NX7103 2.8 28.9 0.8 O A:ASP30 3.0 29.6 1.0 O B:NX7103 3.2 34.1 0.8 O B:HOH218 3.3 38.2 1.0 N B:NX7103 3.5 27.9 0.8 CB A:ASP30 3.5 30.0 1.0 C B:NX7103 3.6 35.8 0.8 C2 B:NX7103 3.6 39.1 0.8 C A:ASP30 3.7 22.5 1.0 OH B:TYR18 3.8 34.4 1.0 C10 B:NX7103 3.9 27.8 0.8 C1 B:NX7103 4.1 40.3 0.8 CE1 B:TYR18 4.2 35.1 1.0 CZ B:TYR18 4.2 34.9 1.0 OE2 B:GLU49 4.2 45.4 1.0 CA A:ASP30 4.2 28.3 1.0 CD B:GLU49 4.4 46.4 1.0 CG B:GLU49 4.5 41.9 1.0 N A:GLY31 4.5 25.2 1.0 C7 B:NX7103 4.6 28.7 0.8 F B:NX7103 4.7 37.7 0.8 N A:ASP30 4.7 28.7 1.0 CA A:GLY31 4.8 27.1 1.0 CG A:ASP30 4.8 31.4 1.0

Fluorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006


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 -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ C:F102 b:42.2 occ:0.54 F C:NX7102 0.0 42.2 0.5 C C:NX7102 1.4 39.4 0.5 C1 C:NX7102 2.4 42.0 0.5 C5 C:NX7102 2.4 38.6 0.5 C6 C:NX7102 2.9 38.4 0.5 OE1 C:GLU49 3.2 65.5 1.0 OH C:TYR18 3.2 43.6 1.0 N C:NX7102 3.4 36.5 0.5 C7 C:NX7102 3.5 34.0 0.5 C4 C:NX7102 3.6 42.0 0.5 C2 C:NX7102 3.6 39.8 0.5 CZ C:TYR18 3.7 32.9 1.0 O C:NX7102 3.7 31.9 0.5 CE2 C:TYR18 3.7 33.9 1.0 CD C:GLU49 4.1 57.9 1.0 C3 C:NX7102 4.1 39.4 0.5 OE2 C:GLU49 4.3 65.7 1.0 C10 C:NX7102 4.5 34.5 0.5 CE1 C:TYR18 4.6 30.0 1.0 F1 C:NX7102 4.7 46.6 0.5 CD2 C:TYR18 4.7 25.8 1.0 O C:HOH222 4.9 43.0 1.0

Fluorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006


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 -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ C:F102 b:46.6 occ:0.54 F1 C:NX7102 0.0 46.6 0.5 C4 C:NX7102 1.3 42.0 0.5 C3 C:NX7102 2.3 39.4 0.5 C5 C:NX7102 2.3 38.6 0.5 C6 C:NX7102 2.8 38.4 0.5 CD2 C:PHE44 3.0 28.1 1.0 O C:NX7102 3.1 31.9 0.5 CE2 C:PHE44 3.2 30.1 1.0 CB C:GLU49 3.3 37.2 1.0 N C:NX7102 3.5 36.5 0.5 O C:THR50 3.5 35.5 1.0 C C:NX7102 3.6 39.4 0.5 C2 C:NX7102 3.6 39.8 0.5 C C:GLU49 3.8 40.1 1.0 N C:THR50 3.9 34.4 1.0 C C:THR50 3.9 31.6 1.0 OE1 C:GLU49 3.9 65.5 1.0 C7 C:NX7102 3.9 34.0 0.5 CG C:PHE44 4.0 27.6 1.0 C1 C:NX7102 4.1 42.0 0.5 O C:GLU49 4.2 35.1 1.0 CB C:ALA51 4.2 33.8 1.0 CA C:GLU49 4.2 38.0 1.0 CZ C:PHE44 4.3 30.9 1.0 CA C:THR50 4.3 36.1 1.0 SD C:MET15 4.4 43.5 1.0 N C:ALA51 4.5 33.9 1.0 C8 C:NX7102 4.5 32.2 0.5 CG C:GLU49 4.6 48.6 1.0 C10 C:NX7102 4.6 34.5 0.5 CD C:GLU49 4.6 57.9 1.0 CB C:PHE44 4.6 26.0 1.0 F C:NX7102 4.7 42.2 0.5 CE C:MET15 4.9 46.4 1.0 CD1 C:PHE44 4.9 25.1 1.0 CA C:ALA51 4.9 32.1 1.0

T.Vantieghem, N.A.Aslam, E.M.Osipov, M.Akele, S.Van Belle, S.Beelen, M.Drexler, T.Paulovcakova, V.Lux, D.Fearon, A.Douangamath, F.Von Delft, F.Christ, V.Veverka, P.Verwilst, A.Van Aerschot, Z.Debyser, S.V.Strelkov. Rational Fragment-Based Design of Compounds Targeting the Pwwp Domain of the Hrp Family. Eur.J.Med.Chem. V. 280 16960 2024.
ISSN: ISSN 0223-5234
PubMed: 39461037
DOI: 10.1016/J.EJMECH.2024.116960