Sodium in PDB 6cdj: Hiv-1 Wild Type Protease with Grl-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand

The structure of Hiv-1 Wild Type Protease with Grl-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand, PDB code: 6cdj 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 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.959, 86.077, 46.157, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 17.3

The structure of Hiv-1 Wild Type Protease with Grl-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand (pdb code 6cdj). 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-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand, PDB code: 6cdj:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-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-03314A, 6-5-5-Ring Fused Umbrella- Like Tetrahydropyranofuran As the P2-Ligand, A Cyclopropylaminobenzothiazole As the P2'-Ligand and 3,5- Difluorophenylmethyl As the P1-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:21.6 occ:1.00 O A:HOH338 2.3 24.8 1.0 O A:ASP60 2.3 15.9 1.0 O A:HOH319 2.3 23.7 1.0 O A:HOH327 2.4 29.0 1.0 O A:HOH358 2.5 25.7 1.0 O A:HOH376 2.7 28.3 1.0 C A:ASP60 3.4 14.8 1.0 N A:ASP60 3.7 14.6 1.0 CA A:ASP60 4.0 14.6 1.0 O A:ARG41 4.1 18.8 1.0 CB A:ASP60 4.4 15.8 1.0 N A:GLN61 4.4 15.1 1.0 CB A:GLN61 4.4 19.2 1.0 NE2 A:GLN61 4.5 53.9 1.0 N A:ARG41 4.5 23.9 1.0 CD1 A:ILE62 4.6 15.1 1.0 O A:GLN61 4.6 18.7 1.0 O A:PRO39 4.7 22.0 1.0 C A:TYR59 4.7 13.1 1.0 CA A:GLN61 4.7 15.9 1.0 C A:GLN61 4.8 15.3 1.0 CA A:GLY40 4.8 25.0 1.0 CG A:ARG41 4.9 51.5 1.0

A.K.Ghosh, P.R Nyalapatla, S.Kovela, K.V.Rao, M.Brindisi, H.L.Osswald, M.Amano, M.Aoki, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Design and Synthesis of Highly Potent Hiv-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems As Novel P2 Ligands: Structure-Activity Studies, Biological and X-Ray Structural Analysis. J. Med. Chem. V. 61 4561 2018.
ISSN: ISSN 1520-4804
PubMed: 29763303
DOI: 10.1021/ACS.JMEDCHEM.8B00298