Chlorine in PDB 6x4a: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor, PDB code: 6x4a was solved by A.H.Chan, V.N.Duong, J.A.Ippolito, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.13 / 2.54
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	161.769, 73.976, 107.899, 90.00, 100.05, 90.00
*R / R_free (%)*	23.2 / 26.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor (pdb code 6x4a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor, PDB code: 6x4a:

Chlorine binding site 1 out of 1 in 6x4a

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Chlorine Binding Sites List in 6x4a

Chlorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Variant in Complex with 5-Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)- Yl)Ethoxy)Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non- Nucleoside Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl601 b:69.8 occ:1.00	CL1	A:7AY601	0.0	69.8	1.0
	CAH	A:7AY601	1.7	56.6	1.0
	CAM	A:7AY601	2.7	56.2	1.0
	CAI	A:7AY601	2.7	53.2	1.0
	CAY	A:7AY601	3.1	60.8	1.0
	CD2	A:LEU100	3.6	54.7	1.0
	CB	A:PRO95	3.7	51.1	1.0
	CD1	A:LEU100	3.9	54.4	1.0
	CD2	A:TYR188	3.9	62.2	1.0
	CAL	A:7AY601	4.0	60.2	1.0
	CAJ	A:7AY601	4.0	56.6	1.0
	CG	A:PRO95	4.2	58.9	1.0
	CE2	A:TYR188	4.3	62.4	1.0
	CG	A:LEU100	4.4	56.6	1.0
	CAZ	A:7AY601	4.4	62.5	1.0
	CAK	A:7AY601	4.5	65.2	1.0
	SG	A:CYS181	4.6	81.2	1.0
	CB	A:CYS181	4.6	61.7	1.0
	CG	A:TYR188	4.7	63.4	1.0

Reference:

V.N.Duong, J.A.Ippolito, A.H.Chan, W.G.Lee, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to Wt and Y181C Reverse Transcriptase Highlights Key Features of the Nnrti Binding Site. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 32643196
DOI: 10.1002/PRO.3910

Page generated: Sat Jul 12 21:32:14 2025

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