Iodine in PDB 9gru: Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30

The structure of Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30, PDB code: 9gru was solved by E.M.Osipov, T.Paulovcakova, S.Beelen, T.Vantieghem, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.091, 41.988, 159.955, 90, 90, 90
R / Rfree (%)	25.7 / 30.2

The binding sites of Iodine atom in the Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30 (pdb code 9gru). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30, PDB code: 9gru:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:I101 b:27.9 occ:0.70 I4 A:PYZ101 0.0 27.9 0.7 C4 A:PYZ101 2.1 30.0 0.7 O A:HOH212 3.1 29.2 1.0 C5 A:PYZ101 3.1 28.9 0.7 C3 A:PYZ101 3.1 29.7 0.7 CE1 A:PHE44 3.7 20.7 1.0 CB A:TYR18 3.8 30.0 1.0 CG A:MET15 4.0 32.8 1.0 CD1 A:PHE44 4.0 19.2 1.0 CB A:TRP21 4.0 20.5 1.0 CB A:MET15 4.1 25.9 1.0 CZ A:PHE44 4.1 21.7 1.0 CD2 A:TYR18 4.2 37.6 1.0 CE3 A:TRP21 4.2 24.8 1.0 N1 A:PYZ101 4.2 31.9 0.7 CG A:TYR18 4.2 36.5 1.0 N2 A:PYZ101 4.3 34.1 0.7 CG A:TRP21 4.3 18.2 1.0 CD2 A:TRP21 4.3 23.3 1.0 SD A:MET15 4.3 32.6 1.0 O A:PRO19 4.7 23.7 1.0 N A:MET15 4.7 24.1 1.0 O A:ALA13 4.7 24.7 1.0 CG A:PHE44 4.8 16.8 1.0 CE2 A:PHE44 4.9 29.6 1.0 CA A:MET15 5.0 28.2 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:I101 b:60.2 occ:0.56 I4 B:PYZ101 0.0 60.2 0.6 C4 B:PYZ101 2.1 29.7 0.6 C5 B:PYZ101 3.1 46.4 0.6 O B:HOH210 3.1 32.7 1.0 C3 B:PYZ101 3.1 28.6 0.6 CB B:TYR18 3.6 31.4 1.0 CE1 B:PHE44 3.7 32.2 1.0 CG B:TYR18 3.8 37.2 1.0 CB B:TRP21 3.8 20.4 1.0 CD2 B:TYR18 3.9 41.4 1.0 CE3 B:TRP21 3.9 24.2 1.0 CD1 B:PHE44 4.0 26.2 1.0 CG B:MET15 4.0 50.9 1.0 CG B:TRP21 4.0 19.8 1.0 CD2 B:TRP21 4.0 23.6 1.0 CB B:MET15 4.0 38.0 1.0 N1 B:PYZ101 4.2 39.7 0.6 N2 B:PYZ101 4.3 37.3 0.6 CE B:MET15 4.4 54.5 1.0 CZ B:PHE44 4.4 33.5 1.0 O B:PRO19 4.6 27.1 1.0 CD1 B:TYR18 4.6 39.0 1.0 O B:ALA13 4.7 24.1 1.0 N B:MET15 4.7 30.5 1.0 CE2 B:TYR18 4.7 49.4 1.0 CZ3 B:TRP21 4.8 21.5 1.0 CG B:PHE44 4.8 26.3 1.0 SD B:MET15 4.8 65.4 1.0 CD1 B:TRP21 4.9 22.0 1.0 CE2 B:TRP21 4.9 24.1 1.0 CA B:MET15 5.0 39.2 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Hrp-2 Pwwp Domain in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:32.4 occ:0.66 I4 C:PYZ101 0.0 32.4 0.7 C4 C:PYZ101 2.1 29.8 0.7 O C:HOH207 3.0 27.3 1.0 C5 C:PYZ101 3.1 29.3 0.7 C3 C:PYZ101 3.1 30.3 0.7 CE C:MET15 3.8 42.5 1.0 CE1 C:PHE44 3.8 42.3 1.0 CB C:TYR18 3.8 25.6 1.0 CB C:TRP21 3.9 24.1 1.0 CG C:TYR18 4.0 30.9 1.0 CE3 C:TRP21 4.0 19.5 1.0 CG C:MET15 4.1 34.6 1.0 CZ C:PHE44 4.1 32.5 1.0 CG C:TRP21 4.1 22.1 1.0 CD2 C:TRP21 4.1 21.7 1.0 CB C:MET15 4.1 29.4 1.0 CD1 C:PHE44 4.2 41.5 1.0 N1 C:PYZ101 4.2 43.5 0.7 N2 C:PYZ101 4.3 46.0 0.7 CD1 C:TYR18 4.3 34.4 1.0 CD2 C:TYR18 4.5 37.9 1.0 SD C:MET15 4.5 45.2 1.0 CE2 C:PHE44 4.7 41.2 1.0 O C:PRO19 4.7 26.3 1.0 O C:ALA13 4.7 27.1 1.0 CG C:PHE44 4.7 33.3 1.0 N C:MET15 4.8 23.4 1.0 CZ3 C:TRP21 4.9 29.3 1.0 CD2 C:PHE44 5.0 46.2 1.0 CD1 C:TRP21 5.0 30.0 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