Magnesium in PDB 6ul5: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor:
2.7.7.49;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor, PDB code: 6ul5 was solved by F.X.Ruiz, A.Pilch, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.27 / 2.23
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	162.488, 73.068, 109.085, 90.00, 100.29, 90.00
*R / R_free (%)*	21.1 / 24.5

Other elements in 6ul5:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor (pdb code 6ul5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor, PDB code: 6ul5:

Magnesium binding site 1 out of 1 in 6ul5

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Magnesium Binding Sites List in 6ul5

Magnesium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with 4-[(4-{4-[(E)-2-Cyanoethenyl]-2,6-Dimethylphenoxy}Thieno[3,2- D]Pyrimidin-2-Yl)Amino]-2-Fluorobenzonitrile (24B), A Non-Nucleoside Rt Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg611 b:62.8 occ:1.00	OD2	A:ASP443	2.1	54.9	1.0
	O	A:HOH831	2.1	60.8	1.0
	O	A:HOH827	2.1	59.7	1.0
	O	A:HOH743	2.2	51.3	1.0
	O	A:HOH760	2.2	56.5	1.0
	CG	A:ASP443	2.9	45.5	1.0
	OD1	A:ASP443	3.0	48.0	1.0
	OD2	A:ASP549	3.1	72.6	1.0
	OD2	A:ASP498	3.4	41.5	1.0
	CG	A:ASP549	3.9	71.5	1.0
	CB	A:ASP549	4.0	67.6	1.0
	CB	A:ASP443	4.3	46.1	1.0
	CG	A:ASP498	4.3	42.7	1.0
	CA	A:ASP549	4.3	67.7	1.0
	OD1	A:ASP498	4.4	42.5	1.0
	O	A:GLY444	4.5	48.3	1.0
	CE1	A:HIS539	4.6	64.0	1.0
	O	A:HOH793	4.7	62.9	1.0
	OG	A:SER553	4.7	75.8	1.0
	NE2	A:HIS539	4.8	57.1	1.0
	OD1	A:ASP549	4.9	68.9	1.0

Reference:

D.Kang, F.X.Ruiz, D.Feng, A.Pilch, T.Zhao, F.Wei, Z.Wang, Y.Sun, Z.Fang, E.De Clercq, C.Pannecouque, E.Arnold, X.Liu, P.Zhan. Discovery and Characterization of Fluorine-Substituted Diarylpyrimidine Derivatives As Novel Hiv-1 Nnrtis with Highly Improved Resistance Profiles and Low Activity For the Herg Ion Channel J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 31935327
DOI: 10.1021/ACS.JMEDCHEM.9B01769

Page generated: Wed Aug 13 18:35:44 2025

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