Sodium in PDB 6e7j: Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand, PDB code: 6e7j 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)	49.10 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.793, 86.043, 45.875, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.2

The structure of Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand (pdb code 6e7j). 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand, PDB code: 6e7j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:24.4 occ:1.00 O A:HOH342 2.3 25.9 1.0 O A:HOH327 2.3 21.7 1.0 O A:ASP60 2.4 17.3 1.0 O A:HOH315 2.4 19.8 0.5 O A:HOH319 2.4 22.0 1.0 O A:HOH350 2.7 29.8 1.0 C A:ASP60 3.4 16.4 1.0 N A:ASP60 3.8 16.7 1.0 CA A:ASP60 4.0 16.6 1.0 O A:ARG41 4.1 20.5 1.0 CB A:GLN61 4.4 22.0 0.6 CB A:GLN61 4.4 19.1 0.4 N A:ARG41 4.4 25.1 1.0 N A:GLN61 4.4 17.4 1.0 CB A:ASP60 4.4 18.8 1.0 O A:GLN61 4.5 20.3 1.0 CD1 A:ILE62 4.6 19.4 1.0 OE1 A:GLN61 4.6 48.8 0.6 O A:PRO39 4.7 26.1 1.0 CA A:GLN61 4.7 18.2 1.0 C A:GLN61 4.7 17.4 1.0 C A:TYR59 4.8 15.0 1.0 CA A:GLY40 4.9 26.2 1.0 C A:ARG41 5.0 20.6 1.0 C A:GLY40 5.0 22.7 1.0

Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand


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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:26.3 occ:1.00 O B:HOH212 2.3 21.8 1.0 O B:ASP60 2.4 18.2 1.0 O B:HOH214 2.4 25.3 1.0 O B:HOH250 2.5 36.8 1.0 O B:HOH269 2.6 25.6 0.5 O B:HOH245 3.0 25.6 0.8 C B:ASP60 3.5 17.1 1.0 N B:ASP60 3.7 15.8 1.0 CA B:ASP60 4.0 17.0 1.0 O B:ARG41 4.1 18.3 1.0 CB B:ASP60 4.4 18.9 1.0 O B:HOH280 4.4 31.7 0.5 O B:PRO39 4.5 21.0 1.0 CB B:GLN61 4.5 20.2 1.0 N B:GLN61 4.6 16.5 1.0 N B:ARG41 4.6 16.1 1.0 C B:TYR59 4.6 14.3 1.0 CA B:GLY40 4.6 18.0 1.0 CD1 B:ILE62 4.8 17.1 1.0 O B:GLN61 4.9 23.5 1.0 C B:GLN61 4.9 17.3 1.0 CA B:GLN61 4.9 17.4 1.0 CA B:TYR59 5.0 13.2 1.0

A.K.Ghosh, J.N.Williams, R.Y.Ho, H.M.Simpson, S.I.Hattori, H.Hayashi, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Design and Synthesis of Potent Hiv-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold As the P2 Ligands: Structure-Activity Studies and Biological and X-Ray Structural Studies. J. Med. Chem. V. 61 9722 2018.
ISSN: ISSN 1520-4804
PubMed: 30354121
DOI: 10.1021/ACS.JMEDCHEM.8B01227