Sodium in PDB 6vod: Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand, PDB code: 6vod 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)	33.43 / 1.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.784, 86.209, 46.015, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.5

The structure of Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand (pdb code 6vod). 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand, PDB code: 6vod:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:20.8 occ:1.00 O A:HOH646 2.3 19.8 1.0 O A:ASP60 2.4 13.7 1.0 O A:HOH622 2.4 17.4 1.0 O A:HOH662 2.4 21.6 1.0 O A:HOH651 2.5 28.5 1.0 O A:HOH684 2.6 27.6 1.0 C A:ASP60 3.4 12.3 1.0 N A:ASP60 3.8 12.2 1.0 CA A:ASP60 4.0 12.4 1.0 O A:HOH640 4.0 30.2 1.0 O A:ARG41 4.1 15.9 1.0 O A:HOH701 4.4 28.0 0.5 CB A:ASP60 4.4 14.8 1.0 N A:GLN61 4.4 13.1 1.0 CB A:GLN61 4.4 16.1 1.0 N A:ARG41 4.5 21.4 1.0 O A:GLN61 4.6 16.3 1.0 O A:PRO39 4.6 20.3 1.0 CD1 A:ILE62 4.7 12.9 1.0 CA A:GLY40 4.7 20.2 1.0 C A:GLN61 4.7 12.6 1.0 C A:TYR59 4.7 10.2 1.0 CA A:GLN61 4.8 12.2 1.0 OE1 A:GLN61 4.9 39.5 1.0 C A:GLY40 5.0 17.6 1.0

A.K.Ghosh, S.Kovela, H.L.Osswald, M.Amano, M.Aoki, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Structure-Based Design of Highly Potent Hiv-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-Ray Structural Studies. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32348139
DOI: 10.1021/ACS.JMEDCHEM.0C00202