Sodium in PDB 5upz: Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz 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 / 1.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.175, 86.418, 45.828, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 19.8

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl 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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group (pdb code 5upz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl 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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:19.6 occ:1.00 O A:HOH355 2.3 20.3 1.0 O A:HOH373 2.3 29.6 1.0 O A:ASP60 2.4 13.6 1.0 O A:HOH371 2.4 22.2 1.0 O A:HOH322 2.4 18.3 1.0 O A:HOH395 2.6 25.3 1.0 C A:ASP60 3.5 13.8 1.0 N A:ASP60 3.8 11.8 1.0 CA A:ASP60 4.1 13.0 1.0 O A:ARG41 4.1 16.2 1.0 O A:HOH340 4.2 21.8 0.5 O A:HOH369 4.2 29.1 0.5 CB A:GLN61 4.3 15.1 1.0 O A:HOH405 4.4 24.6 0.5 CB A:ASP60 4.4 15.6 1.0 N A:ARG41 4.5 19.4 1.0 N A:GLN61 4.5 12.7 1.0 O A:GLN61 4.6 17.3 1.0 O A:HOH354 4.7 24.0 0.5 CD1 A:ILE62 4.7 13.5 1.0 C A:TYR59 4.7 10.2 1.0 O A:PRO39 4.8 18.5 1.0 CA A:GLN61 4.8 13.1 1.0 C A:GLN61 4.8 12.6 1.0 OE1 A:GLN61 4.9 48.8 1.0 CA A:GLY40 4.9 20.2 1.0

Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl 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 2 of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:20.2 occ:0.50 O B:HOH313 2.1 36.9 0.5 O B:HOH224 2.4 28.7 1.0 O B:ASP60 2.4 14.0 1.0 O B:HOH217 2.5 26.5 1.0 O B:HOH281 2.8 23.3 0.5 C B:ASP60 3.5 11.4 1.0 N B:ASP60 3.6 12.5 1.0 O B:HOH278 3.8 30.7 1.0 CA B:ASP60 4.0 13.0 1.0 O B:ARG41 4.2 14.5 1.0 CB B:ASP60 4.3 14.0 1.0 C B:TYR59 4.5 9.5 1.0 O B:PRO39 4.5 16.5 1.0 N B:GLN61 4.6 11.5 1.0 CD1 B:ILE62 4.6 13.1 1.0 CB B:GLN61 4.8 14.5 1.0 CA B:TYR59 4.8 10.2 1.0 N B:ARG41 4.9 12.0 1.0 CA B:GLY40 5.0 14.2 1.0 O B:GLN61 5.0 17.8 1.0 C B:GLN61 5.0 11.5 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