Sodium in PDB 6e9a: Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a 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 / 1.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.372, 86.276, 46.020, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.8

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand (pdb code 6e9a). 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:19.0 occ:1.00 O A:HOH637 2.3 19.5 1.0 O A:ASP60 2.4 13.6 1.0 O A:HOH613 2.4 19.0 1.0 O A:HOH631 2.4 29.6 1.0 O A:HOH651 2.4 20.3 1.0 O A:HOH655 2.7 28.5 1.0 C A:ASP60 3.4 13.1 1.0 N A:ASP60 3.7 12.3 1.0 CA A:ASP60 4.0 12.4 1.0 O A:ARG41 4.2 15.8 1.0 O A:HOH628 4.3 25.4 0.5 CB A:ASP60 4.3 15.2 1.0 CB A:GLN61 4.4 16.4 1.0 N A:GLN61 4.5 13.0 1.0 N A:ARG41 4.5 20.4 1.0 O A:GLN61 4.6 16.6 1.0 C A:TYR59 4.7 10.5 1.0 O A:PRO39 4.7 19.0 1.0 CD1 A:ILE62 4.8 15.0 1.0 CA A:GLN61 4.8 14.0 1.0 CA A:GLY40 4.8 19.6 1.0 C A:GLN61 4.8 13.9 1.0 OE1 A:GLN61 4.8 40.0 1.0 C A:GLY40 5.0 17.8 1.0

Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:19.8 occ:0.50 O B:HOH324 2.3 23.6 1.0 O B:ASP60 2.5 17.6 1.0 O B:HOH355 2.5 39.3 1.0 O B:HOH383 2.5 33.9 0.5 O B:HOH319 2.6 30.1 1.0 C B:ASP60 3.5 15.8 1.0 N B:ASP60 3.6 14.7 1.0 O B:HOH343 3.6 24.8 0.5 CA B:ASP60 3.9 14.6 1.0 O B:ARG41 4.1 15.8 1.0 CB B:ASP60 4.2 16.5 1.0 C B:TYR59 4.5 11.2 1.0 O B:PRO39 4.6 17.7 1.0 N B:GLN61 4.6 14.2 1.0 CD1 B:ILE62 4.7 18.6 1.0 CB B:GLN61 4.8 17.6 1.0 N B:ARG41 4.8 13.0 1.0 CA B:TYR59 4.9 12.3 1.0 CA B:GLY40 4.9 14.7 1.0 C B:GLN61 5.0 15.9 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