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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

Protein crystallography data

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

Other elements in 6cdj:

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

Sodium Binding Sites:

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 6cdj

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 12:02:13 2020

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