Sodium in PDB 6vce: Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.48 / 1.18
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.904, 86.207, 46.090, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 15.5

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand (pdb code 6vce). 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A 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-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:19.3 occ:1.00 O A:HOH648 2.3 18.6 1.0 O A:ASP60 2.4 13.9 1.0 O A:HOH658 2.4 22.7 1.0 O A:HOH619 2.4 19.4 1.0 O A:HOH633 2.5 23.9 0.8 O A:HOH682 2.7 26.1 1.0 C A:ASP60 3.4 13.1 1.0 N A:ASP60 3.8 12.8 1.0 CA A:ASP60 4.1 12.7 1.0 O A:HOH634 4.1 30.6 1.0 O A:ARG41 4.1 16.6 1.0 CB A:ASP60 4.4 14.6 1.0 CB A:GLN61 4.4 16.0 1.0 N A:GLN61 4.4 13.7 1.0 N A:ARG41 4.5 21.3 1.0 O A:GLN61 4.6 15.8 1.0 O A:HOH662 4.6 27.4 0.5 CD1 A:ILE62 4.6 13.0 1.0 O A:PRO39 4.7 20.9 1.0 C A:GLN61 4.7 13.2 1.0 CA A:GLN61 4.7 13.6 1.0 C A:TYR59 4.8 11.1 1.0 CA A:GLY40 4.8 21.2 1.0 OE1 A:GLN61 4.9 38.1 1.0 C A:GLY40 5.0 19.0 1.0

A.K.Ghosh, A.Grillo, J.Raghavaiah, S.Kovela, M.E.Johnson, D.W.Kneller, Y.F.Wang, S.I.Hattori, N.Higashi-Kuwata, I.T.Weber, H.Mitsuya. Design, Synthesis, and X-Ray Studies of Potent Hiv-1 Protease Inhibitors with P2-Carboxamide Functionalities. Acs Med.Chem.Lett. V. 11 1965 2020.
ISSN: ISSN 1948-5875
PubMed: 33062180
DOI: 10.1021/ACSMEDCHEMLETT.9B00670