Sodium in PDB 8fuj: Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group, PDB code: 8fuj 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) 36.30 / 1.12
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.609, 86.214, 46.189, 90, 90, 90
R / Rfree (%) 12.1 / 13.6

Other elements in 8fuj:

The structure of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group (pdb code 8fuj). 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-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group, PDB code: 8fuj:

Sodium binding site 1 out of 1 in 8fuj

Go back to Sodium Binding Sites List in 8fuj
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 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-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:15.1
occ:0.90
 O A:HOH640 2.3 16.3 1.0
O A:ASP60 2.4 10.7 1.0
O A:HOH681 2.4 18.5 0.7
O A:HOH615 2.4 15.8 1.0
O A:HOH677 2.4 19.0 1.0
O A:HOH700 2.6 24.1 1.0
C A:ASP60 3.4 9.4 1.0
N A:ASP60 3.8 9.1 1.0
NE2 A:GLN61 3.9 26.9 0.3
CA A:ASP60 4.0 9.9 1.0
O A:HOH659 4.1 20.1 0.6
O A:ARG41 4.1 13.3 1.0
CB A:GLN61 4.3 12.9 0.3
CB A:GLN61 4.4 13.0 0.7
CB A:ASP60 4.4 12.4 1.0
N A:GLN61 4.4 10.0 1.0
O A:HOH716 4.4 24.5 0.5
N A:ARG41 4.5 16.1 1.0
O A:HOH735 4.5 26.3 0.5
O A:GLN61 4.6 12.7 1.0
O A:PRO39 4.7 15.4 1.0
CA A:GLN61 4.7 10.9 0.3
CA A:GLN61 4.7 10.9 0.7
CD1 A:ILE62 4.7 9.5 1.0
C A:TYR59 4.7 7.9 1.0
C A:GLN61 4.8 10.2 1.0
CA A:GLY40 4.8 18.1 1.0
CD A:GLN61 4.9 25.5 0.3
OE1 A:GLN61 4.9 30.8 0.7

Reference:

A.K.Ghosh, J.L.Mishevich, S.Kovela, R.Shaktah, A.K.Ghosh, M.Johnson, Y.F.Wang, A.Wong-Sam, J.Agniswamy, M.Amano, Y.Takamatsu, S.I.Hattori, I.T.Weber, H.Mitsuya. Exploration of Imatinib and Nilotinib-Derived Templates As the P2-Ligand For Hiv-1 Protease Inhibitors: Design, Synthesis, Protein X-Ray Structural Studies, and Biological Evaluation. Eur.J.Med.Chem. V. 255 15385 2023.
ISSN: ISSN 0223-5234
PubMed: 37150084
DOI: 10.1016/J.EJMECH.2023.115385
Page generated: Fri Jul 28 03:28:10 2023

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