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Sodium in PDB 8f0f: Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group, PDB code: 8f0f was solved by Y.-F.Wang, J.Agniswamy, A.K.Ghosh, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.72 / 1.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.419, 86.235, 46.075, 90, 90, 90
R / Rfree (%) 13.2 / 16.3

Other elements in 8f0f:

The structure of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group (pdb code 8f0f). 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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group, PDB code: 8f0f:

Sodium binding site 1 out of 1 in 8f0f

Go back to Sodium Binding Sites List in 8f0f
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group


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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:23.2
occ:1.00
 O A:HOH634 2.2 16.0 1.0
O A:ASP60 2.4 14.6 1.0
O A:HOH674 2.4 18.0 1.0
O A:HOH620 2.4 14.1 0.8
O A:HOH659 2.5 16.6 0.5
O A:HOH686 2.7 19.7 1.0
C A:ASP60 3.4 12.7 1.0
N A:ASP60 3.8 12.8 1.0
CA A:ASP60 4.0 13.4 1.0
O A:HOH646 4.1 26.6 0.5
O A:ARG41 4.2 17.1 1.0
CB A:ASP60 4.4 17.2 1.0
CB A:GLN61 4.4 16.5 1.0
N A:GLN61 4.4 13.3 1.0
N A:ARG41 4.6 21.4 1.0
O A:HOH683 4.6 29.2 0.5
O A:PRO39 4.6 20.7 1.0
O A:GLN61 4.6 16.8 1.0
CD1 A:ILE62 4.7 13.4 1.0
C A:TYR59 4.7 11.4 1.0
C A:GLN61 4.8 12.9 1.0
CA A:GLN61 4.8 13.9 1.0
CA A:GLY40 4.8 22.4 1.0
OE1 A:GLN61 5.0 43.8 1.0

Reference:

A.K.Ghosh, D.Shahabi, M.Kipfmiller, A.K.Ghosh, M.Johnson, Y.F.Wang, J.Agniswamy, M.Amano, I.T.Weber, H.Mitsuya. Evaluation of Darunavir-Derived Hiv-1 Protease Inhibitors Incorporating P2' Amide-Derivatives: Synthesis, Biological Evaluation and Structural Studies. Bioorg.Med.Chem.Lett. 29168 2023.
ISSN: ESSN 1464-3405
PubMed: 36738797
DOI: 10.1016/J.BMCL.2023.129168
Page generated: Wed Oct 9 11:47:49 2024

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