Fluorine in PDB 7gib: Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064)

Enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064)

All present enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064):
3.4.22.69;

Protein crystallography data

The structure of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064), PDB code: 7gib was solved by D.Fearon, A.Aimon, J.C.Aschenbrenner, B.H.Balcomb, F.K.R.Bertram, J.Brandao-Neto, A.Dias, A.Douangamath, L.Dunnett, A.S.Godoy, T.J.Gorrie-Stone, L.Koekemoer, T.Krojer, R.M.Lithgo, P.Lukacik, P.G.Marples, H.Mikolajek, E.Nelson, C.D.Owen, A.J.Powell, V.L.Rangel, R.Skyner, C.M.Strain-Damerell, W.Thompson, C.W.E.Tomlinson, C.Wild, M.A.Walsh, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	71.52 / 1.68
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	67.28, 99.06, 103.35, 90, 90, 90
*R / R_free (%)*	22.9 / 25.7

Other elements in 7gib:

Chlorine

(Cl)

1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064) (pdb code 7gib). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064), PDB code: 7gib:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7gib

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Fluorine Binding Sites List in 7gib

Fluorine binding site 1 out of 2 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064)

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F404 b:40.8 occ:1.00	F	A:QER404	0.0	40.8	1.0
	C	A:QER404	1.4	39.9	1.0
	C16	A:QER404	2.3	38.7	1.0
	C1	A:QER404	2.3	39.8	1.0
	CA	A:ASP187	3.3	32.2	1.0
	CB	A:ASP187	3.3	31.5	1.0
	CD2	A:HIS41	3.4	34.6	1.0
	C2	A:QER404	3.6	39.6	1.0
	C4	A:QER404	3.6	38.2	1.0
	CB	A:MET165	3.8	33.0	1.0
	SD	A:MET165	3.8	46.9	1.0
	C	A:ASP187	3.8	34.0	1.0
	O	A:HIS164	3.9	28.4	1.0
	CE	A:MET49	4.0	51.2	1.0
	NE2	A:HIS41	4.0	35.5	1.0
	C3	A:QER404	4.1	39.2	1.0
	CE	A:MET165	4.1	35.5	1.0
	CG	A:HIS41	4.2	33.1	1.0
	CG	A:MET165	4.3	37.0	1.0
	N	A:ARG188	4.3	35.0	1.0
	C	A:HIS164	4.4	28.2	1.0
	O	A:ASP187	4.4	34.7	1.0
	CB	A:HIS164	4.4	27.2	1.0
	N	A:ASP187	4.6	32.5	1.0
	CB	A:HIS41	4.6	30.8	1.0
	O	A:VAL186	4.7	33.0	1.0
	O	A:HOH571	4.7	26.1	1.0
	CA	A:MET165	4.8	30.8	1.0
	CG	A:ASP187	4.8	30.9	1.0
	CE1	A:HIS41	4.8	35.2	1.0
	N	A:MET165	4.8	29.2	1.0
	C5	A:QER404	4.9	37.1	1.0
	ND1	A:HIS41	5.0	34.7	1.0
	CZ	A:PHE181	5.0	29.3	1.0

Fluorine binding site 2 out of 2 in 7gib

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Fluorine Binding Sites List in 7gib

Fluorine binding site 2 out of 2 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064)

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Ral-Tha-2D450E86-10 (Mpro-P0064) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F404 b:39.1 occ:1.00	F	B:QER404	0.0	39.1	1.0
	C	B:QER404	1.4	39.2	1.0
	C16	B:QER404	2.3	39.2	1.0
	C1	B:QER404	2.3	39.4	1.0
	CA	B:ASP187	3.2	32.2	1.0
	CB	B:ASP187	3.4	31.6	1.0
	C2	B:QER404	3.6	39.9	1.0
	C4	B:QER404	3.6	39.2	1.0
	C	B:ASP187	3.7	33.8	1.0
	CD2	B:HIS41	3.7	34.6	1.0
	CB	B:MET165	3.7	30.0	1.0
	SD	B:MET165	3.7	50.2	1.0
	N	B:ARG188	3.9	34.5	1.0
	CE	B:MET165	4.0	34.5	1.0
	CE	B:MET49	4.0	51.3	1.0
	O	B:HIS164	4.0	28.1	1.0
	C3	B:QER404	4.1	39.7	1.0
	CG	B:MET165	4.2	35.6	1.0
	NE2	B:HIS41	4.2	36.1	1.0
	O	B:ASP187	4.4	34.5	1.0
	CG	B:HIS41	4.4	33.9	1.0
	O	B:VAL186	4.4	31.6	1.0
	N	B:ASP187	4.5	31.2	1.0
	C	B:HIS164	4.5	27.0	1.0
	CB	B:HIS164	4.6	25.8	1.0
	CA	B:MET165	4.8	27.8	1.0
	CB	B:HIS41	4.8	31.7	1.0
	C5	B:QER404	4.9	38.6	1.0
	CG	B:ASP187	4.9	33.4	1.0
	O	B:HOH527	4.9	26.9	1.0
	C	B:VAL186	4.9	31.1	1.0
	N	B:MET165	4.9	26.6	1.0
	CA	B:ARG188	5.0	35.7	1.0
	CZ	B:PHE181	5.0	27.1	1.0

Reference:

M.L.Boby, D.Fearon, M.Ferla, M.Filep, L.Koekemoer, M.C.Robinson, The Covid Moonshot Consortium, J.D.Chodera, A.A.Lee, N.London, A.Von Delft, F.Von Delft. Open Science Discovery of Potent Noncovalent Sars-Cov-2 Main Protease Inhibitors Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABO7201

Page generated: Tue Jul 15 20:12:20 2025

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