Sodium in PDB 5uov: Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group

The structure of Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group, PDB code: 5uov was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.33
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.179, 86.515, 45.945, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.3

The structure of Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group (pdb code 5uov). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group, PDB code: 5uov:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-1118A , An Isophthalamide-Derived P2-P3 Ligand with the Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:22.2 occ:1.00 O A:HOH334 2.3 20.2 1.0 O A:HOH345 2.3 32.9 1.0 O A:ASP60 2.3 14.5 1.0 O A:HOH321 2.4 19.6 1.0 O A:HOH347 2.5 24.6 1.0 O A:HOH364 2.8 30.4 1.0 C A:ASP60 3.4 13.0 1.0 N A:ASP60 3.7 12.8 1.0 CA A:ASP60 4.0 13.0 1.0 O A:ARG41 4.2 16.1 1.0 O A:HOH356 4.3 32.3 0.5 CB A:GLN61 4.4 16.4 1.0 CB A:ASP60 4.4 15.5 1.0 N A:GLN61 4.4 12.9 1.0 N A:ARG41 4.5 19.4 1.0 O A:HOH370 4.6 33.3 0.5 CD1 A:ILE62 4.6 15.9 1.0 C A:TYR59 4.6 9.7 1.0 O A:PRO39 4.7 20.1 1.0 O A:GLN61 4.7 17.4 1.0 CA A:GLN61 4.8 13.4 1.0 C A:GLN61 4.8 13.3 1.0 OE1 A:GLN61 4.9 44.9 1.0 CA A:GLY40 4.9 22.1 1.0

A.K.Ghosh, M.Brindisi, P.R.Nyalapatla, J.Takayama, J.R.Ella-Menye, S.Yashchuk, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design of Novel Hiv-1 Protease Inhibitors Incorporating Isophthalamide-Derived P2-P3 Ligands: Synthesis, Biological Evaluation and X-Ray Structural Studies of Inhibitor-Hiv-1 Protease Complex. Bioorg. Med. Chem. V. 25 5114 2017.
ISSN: ESSN 1464-3391
PubMed: 28434781
DOI: 10.1016/J.BMC.2017.04.005