Sodium in PDB 6b4n: A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands

The structure of A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands, PDB code: 6b4n 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 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.990, 86.399, 45.760, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.6

The structure of A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands (pdb code 6b4n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands, PDB code: 6b4n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the 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 Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:17.6 occ:1.00 O A:HOH341 2.3 15.9 1.0 O A:HOH344 2.4 28.0 1.0 O A:HOH355 2.4 18.9 1.0 O A:ASP60 2.4 12.0 1.0 O A:HOH324 2.5 17.2 1.0 O A:HOH375 2.7 24.7 1.0 C A:ASP60 3.5 11.1 1.0 N A:ASP60 3.8 9.8 1.0 CA A:ASP60 4.1 11.3 1.0 O A:ARG41 4.1 15.3 1.0 O A:HOH343 4.2 22.4 0.5 CB A:GLN61 4.4 16.4 1.0 CB A:ASP60 4.5 14.5 1.0 N A:ARG41 4.5 17.7 1.0 N A:GLN61 4.5 11.5 1.0 O A:HOH374 4.5 37.0 1.0 O A:HOH385 4.5 25.3 0.5 O A:GLN61 4.6 15.3 1.0 O A:PRO39 4.7 17.5 1.0 CD1 A:ILE62 4.7 13.0 1.0 C A:GLN61 4.7 11.9 1.0 C A:TYR59 4.8 9.9 1.0 CA A:GLN61 4.8 12.1 1.0 CA A:GLY40 4.8 18.2 1.0 OE1 A:GLN61 4.9 54.4 1.0

Sodium binding site 2 out of 2 in the A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Hydroxymethyl Functionality at the 4-Position of the 2-Phenyloxazole Moiety of Hiv-1 Protease Inhibitors Involving the P2' Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:26.2 occ:0.50 O B:HOH209 2.2 22.8 0.5 O B:HOH232 2.2 31.6 1.0 O B:HOH202 2.4 33.5 1.0 O B:HOH224 2.7 17.6 1.0 OH B:TYR59 3.8 14.9 1.0 OG B:SER37 4.0 24.0 0.4 CA B:SER37 4.0 19.0 0.4 O B:HOH211 4.1 19.8 1.0 OG B:SER37 4.1 30.3 0.6 CA B:SER37 4.1 19.2 0.6 CB B:SER37 4.2 22.3 0.4 N B:LEU38 4.2 15.3 1.0 O B:LEU38 4.2 14.3 1.0 NH2 B:ARG57 4.4 19.8 1.0 O B:HOH214 4.4 35.2 0.5 CB B:SER37 4.5 22.1 0.6 O B:MET36 4.7 17.6 1.0 C B:SER37 4.7 16.6 1.0 CZ B:TYR59 4.9 12.3 1.0

A.K.Ghosh, W.S.Fyvie, M.Brindisi, M.Steffey, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design, Synthesis, Biological Evaluation, and X-Ray Studies of Hiv-1 Protease Inhibitors with Modified P2' Ligands of Darunavir. Chemmedchem V. 12 1942 2017.
ISSN: ESSN 1860-7187
PubMed: 29110408
DOI: 10.1002/CMDC.201700614