Sodium in PDB 7to5: Hiv-1 Wild Type Protease with Grl-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1]

The structure of Hiv-1 Wild Type Protease with Grl-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1], PDB code: 7to5 was solved by Y.-F.Wang, J.Agniswamy, A.K.Ghosh, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.34 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.943, 86.138, 46.097, 90, 90, 90
R / Rfree (%)	12.3 / 14.2

The structure of Hiv-1 Wild Type Protease with Grl-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1] 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-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1] (pdb code 7to5). 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-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1], PDB code: 7to5:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1]


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-05816A, with C-4 Substituted Cyclohexane-Fused Bis-Tetrahydrofuran (Chf-Thf) Derivatives As P2- Ligand [Diastereomer 1] within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:16.8 occ:0.80 O A:HOH634 2.3 18.7 1.0 O A:ASP60 2.4 11.8 1.0 O A:HOH666 2.4 25.9 1.0 O A:HOH673 2.4 21.6 1.0 O A:HOH613 2.4 18.2 1.0 O A:HOH692 2.6 25.9 1.0 C A:ASP60 3.4 10.9 1.0 N A:ASP60 3.8 10.6 1.0 CA A:ASP60 4.0 10.8 1.0 O A:HOH656 4.1 30.8 1.0 O A:ARG41 4.1 15.7 1.0 O A:HOH712 4.3 26.1 0.5 CB A:ASP60 4.4 12.7 1.0 CB A:GLN61 4.4 14.6 1.0 N A:GLN61 4.4 11.2 1.0 N A:ARG41 4.5 20.4 1.0 O A:PRO39 4.6 19.1 1.0 O A:GLN61 4.6 14.0 1.0 O A:HOH728 4.6 28.1 0.5 CD1 A:ILE62 4.7 11.7 1.0 C A:TYR59 4.7 9.3 1.0 CA A:GLN61 4.7 12.0 1.0 CA A:GLY40 4.8 20.7 1.0 C A:GLN61 4.8 11.1 1.0 OE1 A:GLN61 4.9 39.5 1.0 C A:GLY40 4.9 17.3 1.0

A.K.Ghosh, S.Kovela, A.Sharma, D.Shahabi, A.K.Ghosh, D.R.Hopkins, M.Yadav, M.E.Johnson, J.Agniswamy, Y.F.Wang, S.I.Hattori, N.Higashi-Kuwata, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design, Synthesis and X-Ray Structural Studies of Potent Hiv-1 Protease Inhibitors Containing C-4 Substituted Tricyclic Hexahydro-Furofuran Derivatives As P2 Ligands. Chemmedchem V. 17 00058 2022.
ISSN: ESSN 1860-7187
PubMed: 35170223
DOI: 10.1002/CMDC.202200058