Fluorine in PDB 8udf: Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

All present enzymatic activity of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7, PDB code: 8udf was solved by F.Forouhar, H.Liu, A.Zack, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.07 / 1.74
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	98.087, 81.861, 51.856, 90, 114.81, 90
*R / R_free (%)*	16.5 / 19.4

Other elements in 8udf:

The structure of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7 also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7 (pdb code 8udf). 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 Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7, PDB code: 8udf:

Fluorine binding site 1 out of 1 in 8udf

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Fluorine Binding Sites List in 8udf

Fluorine binding site 1 out of 1 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F701 b:59.6 occ:1.00	F1	A:WB0701	0.0	59.6	1.0
	C9	A:WB0701	1.3	55.2	1.0
	C10	A:WB0701	2.4	47.0	1.0
	C8	A:WB0701	2.5	59.0	1.0
	O	A:HOH848	3.3	57.3	1.0
	C	A:THR496	3.4	42.4	1.0
	N	A:ALA497	3.5	42.4	1.0
	CA	A:THR496	3.6	40.5	1.0
	O	A:HOH881	3.6	51.7	1.0
	C11	A:WB0701	3.6	49.1	1.0
	O	A:GLN495	3.7	41.2	1.0
	O	A:HOH971	3.7	73.2	1.0
	C7	A:WB0701	3.7	55.2	1.0
	C	A:GLN495	3.7	41.2	1.0
	N	A:THR496	3.7	39.5	1.0
	O	A:THR496	3.9	43.1	1.0
	CG	A:GLN495	4.0	49.1	1.0
	C6	A:WB0701	4.2	47.0	1.0
	CA	A:ALA497	4.2	45.6	1.0
	CA	A:GLN495	4.6	40.0	1.0
	CB	A:ALA497	4.6	49.2	1.0
	CB	A:GLN495	4.9	44.0	1.0

Reference:

H.Liu, A.Zack, F.Forouhar, S.Iketani, A.Williams, D.R.Vaz, D.L.Habashi, K.Choi, S.J.Resnick, A.Chavez, D.D.Ho, B.R.Stockwell. Development of Small Molecule Non-Covalent Coronavirus 3CL Protease Inhibitors From Dna-Encoded Chemical Library Screening To Be Published.

Page generated: Wed Jul 16 09:14:19 2025

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