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 / R_free (%)*	12.1 / 13.6

Other elements in 8fuj:

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

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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: Mon Aug 18 14:14:17 2025

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