Sodium in PDB 5wlo: A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands

The structure of A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands, PDB code: 5wlo 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 / 1.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.475, 86.034, 45.877, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 20.5

The structure of A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands (pdb code 5wlo). 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 A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands, PDB code: 5wlo:

Sodium binding site 1 out of 1 in the A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Novel 13-Ring Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:21.5 occ:1.00 O A:HOH634 2.2 23.0 1.0 O A:HOH642 2.3 22.4 1.0 O A:ASP60 2.4 14.8 1.0 O A:HOH646 2.5 23.5 1.0 O A:HOH604 2.5 28.8 1.0 O A:HOH673 2.7 33.8 1.0 C A:ASP60 3.4 14.3 1.0 N A:ASP60 3.7 14.1 1.0 CA A:ASP60 4.0 14.5 1.0 O A:HOH653 4.0 23.5 0.5 O A:ARG41 4.1 20.0 1.0 CB A:GLN61 4.4 16.2 1.0 CB A:ASP60 4.4 16.7 1.0 N A:GLN61 4.5 14.3 1.0 N A:ARG41 4.5 24.5 1.0 O A:GLN61 4.6 16.7 1.0 NE2 A:GLN61 4.6 42.7 1.0 C A:TYR59 4.7 13.7 1.0 O A:PRO39 4.7 22.5 1.0 CD1 A:ILE62 4.7 16.5 1.0 C A:GLN61 4.7 15.6 1.0 CA A:GLN61 4.8 14.5 1.0 CA A:GLY40 4.9 24.4 1.0

A.K.Ghosh, W.Sean Fyvie, M.Brindisi, M.Steffey, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design, Synthesis, X-Ray Studies, and Biological Evaluation of Novel Macrocyclic Hiv-1 Protease Inhibitors Involving the P1'-P2' Ligands. Bioorg. Med. Chem. Lett. V. 27 4925 2017.
ISSN: ESSN 1464-3405
PubMed: 28958624
DOI: 10.1016/J.BMCL.2017.09.003