Fluorine in PDB 9cdm: Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61

Enzymatic activity of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61

All present enzymatic activity of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdm was solved by S.Tang, J.R.Kenneson, K.Huynh, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.34 / 2.05
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	115.665, 54.346, 44.524, 90, 101.11, 90
*R / R_free (%)*	19.4 / 23.7

Other elements in 9cdm:

The structure of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 (pdb code 9cdm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61, PDB code: 9cdm:

Fluorine binding site 1 out of 1 in 9cdm

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Fluorine Binding Sites List in 9cdm

Fluorine binding site 1 out of 1 in the Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Mpro L50F Mutant in Complex with Small Molecule Inhibitor MPRO61 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F401 b:11.4 occ:0.80	F1	A:XEK401	0.0	11.4	0.8
	C6	A:XEK401	1.4	16.7	0.8
	C5	A:XEK401	2.3	11.4	0.8
	C7	A:XEK401	2.4	15.2	0.8
	O2	A:XEK401	2.8	18.0	0.8
	C	A:ARG188	2.9	16.6	1.0
	CL1	A:XEK401	2.9	13.3	0.8
	O	A:ARG188	3.0	15.2	1.0
	N	A:GLN189	3.1	11.8	1.0
	CA	A:ARG188	3.5	15.0	1.0
	N	A:ARG188	3.5	9.6	1.0
	C4	A:XEK401	3.6	8.6	0.8
	CA	A:GLN189	3.6	19.7	1.0
	C15	A:XEK401	3.6	11.8	0.8
	H4	A:XEK401	3.8	21.2	0.8
	C8	A:XEK401	4.0	17.6	0.8
	C	A:ASP187	4.0	9.7	1.0
	SD	A:MET165	4.0	17.6	1.0
	CB	A:GLN189	4.1	20.1	1.0
	C10	A:XEK401	4.1	17.1	0.8
	C3	A:XEK401	4.1	11.8	0.8
	C9	A:XEK401	4.2	17.0	0.8
	H3	A:XEK401	4.3	21.9	0.8
	H1	A:XEK401	4.4	11.0	0.8
	H8	A:XEK401	4.4	14.9	0.8
	CA	A:ASP187	4.5	9.6	1.0
	O	A:ASP187	4.5	11.2	1.0
	O	A:MET49	4.7	25.0	1.0
	H2	A:XEK401	4.7	21.9	0.8
	O	A:VAL186	4.8	10.0	1.0
	C11	A:XEK401	4.9	16.9	0.8
	SD	A:MET49	5.0	40.5	1.0
	CB	A:ARG188	5.0	13.7	1.0

Reference:

J.R.Kenneson, C.Papini, S.Tang, K.Huynh, C.H.Zhang, W.L.Jorgensen, K.S.Anderson. Exploring Possible Drug-Resistant Variants of Sars-Cov-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, MPRO61 Acs Bio Med Chem Au 2025.
ISSN: ESSN 2694-2437
DOI: 10.1021/ACSBIOMEDCHEMAU.4C00109

Page generated: Wed Jul 16 10:42:49 2025

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