Sodium in PDB 5dgu: Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A

The structure of Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A, PDB code: 5dgu was solved by J.Agniswamy, Y.-F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.642, 86.329, 45.981, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 20.1

The structure of Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A (pdb code 5dgu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A, PDB code: 5dgu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:21.3 occ:1.00 O A:HOH324 2.3 20.9 1.0 O A:HOH379 2.3 31.2 1.0 O A:HOH330 2.4 22.1 1.0 O A:ASP60 2.4 15.2 1.0 O A:HOH349 2.4 23.1 1.0 O A:HOH362 2.8 28.4 1.0 C A:ASP60 3.4 13.5 1.0 N A:ASP60 3.8 13.2 1.0 O A:HOH339 3.9 27.1 0.5 CA A:ASP60 4.0 13.8 1.0 O A:ARG41 4.1 19.2 1.0 CB A:ASP60 4.4 15.8 1.0 CB A:GLN61 4.4 16.9 1.0 N A:GLN61 4.5 14.2 1.0 N A:ARG41 4.5 21.5 1.0 O A:GLN61 4.6 18.3 1.0 O A:PRO39 4.7 22.4 1.0 CD1 A:ILE62 4.7 16.7 1.0 C A:TYR59 4.7 12.4 1.0 C A:GLN61 4.8 15.0 1.0 CA A:GLN61 4.8 15.5 1.0 CA A:GLY40 4.8 23.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligand Grl-004-11A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:25.1 occ:0.50 O B:HOH225 2.4 27.7 1.0 O B:HOH224 2.4 31.3 1.0 O B:ASP60 2.4 16.9 1.0 O B:HOH227 2.5 26.1 0.5 C B:ASP60 3.4 14.6 1.0 N B:ASP60 3.6 14.8 1.0 CA B:ASP60 3.9 14.9 1.0 O B:HOH257 4.1 32.9 1.0 CB B:ASP60 4.3 17.0 1.0 O B:ARG41 4.3 16.4 1.0 C B:TYR59 4.6 11.9 1.0 N B:GLN61 4.6 14.6 1.0 O B:PRO39 4.6 18.3 1.0 O B:HOH258 4.7 26.7 0.5 CB B:GLN61 4.7 17.5 1.0 CD1 B:ILE62 4.8 17.3 1.0 CA B:TYR59 4.9 11.5 1.0 O B:GLN61 4.9 19.6 1.0 C B:GLN61 4.9 14.9 1.0 CA B:GLN61 5.0 14.7 1.0 CA B:GLY40 5.0 15.8 1.0 N B:ARG41 5.0 14.5 1.0

A.K.Ghosh, C.D.Martyr, L.A.Kassekert, P.R.Nyalapatla, M.Steffey, J.Agniswamy, Y.F.Wang, I.T.Weber, M.Amano, H.Mitsuya. Design, Synthesis, Biological Evaluation and X-Ray Structural Studies of Hiv-1 Protease Inhibitors Containing Substituted Fused-Tetrahydropyranyl Tetrahydrofuran As P2-Ligands. Org.Biomol.Chem. V. 13 11607 2015.
ISSN: ESSN 1477-0539
PubMed: 26462551
DOI: 10.1039/C5OB01930C