Sodium in PDB 6dv4: Hiv-1 Wild Type Protease with Grl-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand, PDB code: 6dv4 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 / 1.14
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.755, 86.229, 46.181, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.6

The structure of Hiv-1 Wild Type Protease with Grl-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand (pdb code 6dv4). 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-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand, PDB code: 6dv4:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand


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-04315A, A Tetrahydronaphthalene Carboxamide with (R)-Boc-Amine and (S)-Hydroxyl Functionalities As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:22.4 occ:1.00 O A:HOH630 2.3 22.9 1.0 O A:ASP60 2.4 16.5 1.0 O A:HOH639 2.4 27.8 1.0 O A:HOH609 2.4 21.3 1.0 O A:HOH621 2.4 31.8 1.0 O A:HOH638 2.8 38.5 1.0 C A:ASP60 3.4 15.1 1.0 N A:ASP60 3.8 14.4 1.0 CA A:ASP60 4.0 16.1 1.0 O A:ARG41 4.2 19.0 1.0 CB A:GLN61 4.4 18.3 1.0 CB A:ASP60 4.4 18.7 1.0 N A:GLN61 4.4 15.7 1.0 N A:ARG41 4.5 21.7 1.0 O A:GLN61 4.6 19.1 1.0 O A:PRO39 4.6 21.4 1.0 CD1 A:ILE62 4.7 15.5 1.0 C A:TYR59 4.7 12.3 1.0 CA A:GLN61 4.8 15.6 1.0 C A:GLN61 4.8 15.5 1.0 CA A:GLY40 4.8 21.7 1.0 OE1 A:GLN61 4.8 41.1 1.0 O A:HOH658 4.9 34.4 0.5

A.K.Ghosh, R.D.Jadhav, H.Simpson, S.Kovela, H.Osswald, J.Agniswamy, Y.F.Wang, S.I.Hattori, I.T.Weber, H.Mitsuya. Design, Synthesis, and X-Ray Studies of Potent Hiv-1 Protease Inhibitors Incorporating Aminothiochromane and Aminotetrahydronaphthalene Carboxamide Derivatives As the P2 Ligands. Eur J Med Chem V. 160 171 2018.
ISSN: ISSN 1768-3254
PubMed: 30340140
DOI: 10.1016/J.EJMECH.2018.09.046