Chlorine 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
Fluorine	(F)	1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7, PDB code: 8udf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8udf

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Chlorine Binding Sites List in 8udf

Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

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 Sars-Cov-2 3CL Protease with Inhibitor DEL_7 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl701 b:73.3 occ:1.00	CL1	A:WB0701	0.0	73.3	1.0
	C18	A:WB0701	1.7	59.1	1.0
	C17	A:WB0701	2.7	41.9	1.0
	C19	A:WB0701	2.8	54.0	1.0
	ND1	A:HIS347	3.3	37.5	1.0
	CB	A:ASP493	3.4	26.6	1.0
	CA	A:ASP493	3.5	32.1	1.0
	C	A:ASP493	3.5	36.2	1.0
	CE	A:MET355	3.6	66.9	1.0
	CG	A:HIS347	3.6	34.6	1.0
	N	A:ARG494	3.8	31.6	1.0
	CE1	A:HIS347	3.8	35.0	1.0
	O	A:ASP493	3.8	35.4	1.0
	CB	A:HIS347	3.9	30.8	1.0
	C16	A:WB0701	4.0	42.8	1.0
	C20	A:WB0701	4.1	50.2	1.0
	O	A:HIS470	4.3	31.4	1.0
	CD2	A:HIS347	4.3	36.2	1.0
	CA	A:ARG494	4.4	34.2	1.0
	NE2	A:HIS347	4.4	35.6	1.0
	O	A:HOH900	4.5	27.1	1.0
	C15	A:WB0701	4.5	42.3	1.0
	SD	A:MET355	4.6	63.7	1.0
	OH	A:TYR360	4.6	35.3	1.0
	C	A:ARG494	4.6	37.0	1.0
	CG	A:ASP493	4.8	29.2	1.0
	CB	A:MET471	4.8	27.8	1.0
	O	A:ARG494	4.8	35.4	1.0
	SD	A:MET471	4.8	57.5	1.0
	N	A:ASP493	4.9	28.2	1.0

Chlorine binding site 2 out of 4 in 8udf

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Chlorine Binding Sites List in 8udf

Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 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:Cl701 b:48.8 occ:1.00	CL2	A:WB0701	0.0	48.8	1.0
	C16	A:WB0701	1.7	42.8	1.0
	C17	A:WB0701	2.7	41.9	1.0
	C15	A:WB0701	2.7	42.3	1.0
	C14	A:WB0701	3.1	40.1	1.0
	CE	A:MET471	3.3	49.7	1.0
	C10	A:WB0701	3.4	47.0	1.0
	C11	A:WB0701	3.5	49.1	1.0
	C13	A:WB0701	3.6	37.7	1.0
	O	A:HOH910	3.9	42.5	1.0
	C18	A:WB0701	4.0	59.1	1.0
	O	A:ARG494	4.0	35.4	1.0
	CA	A:GLN495	4.0	40.0	1.0
	C20	A:WB0701	4.0	50.2	1.0
	O	A:GLU472	4.1	33.1	1.0
	CB	A:MET471	4.1	27.8	1.0
	N2	A:WB0701	4.2	37.9	1.0
	C12	A:WB0701	4.3	42.6	1.0
	O	A:THR496	4.4	43.1	1.0
	C9	A:WB0701	4.5	55.2	1.0
	SD	A:MET471	4.5	57.5	1.0
	CG	A:GLN495	4.5	49.1	1.0
	C19	A:WB0701	4.5	54.0	1.0
	N	A:THR496	4.6	39.5	1.0
	CB	A:GLN495	4.6	44.0	1.0
	C	A:ARG494	4.7	37.0	1.0
	C6	A:WB0701	4.7	47.0	1.0
	C	A:GLN495	4.7	41.2	1.0
	N	A:GLN495	4.7	35.5	1.0
	N3	A:WB0701	4.8	37.2	1.0
	CG	A:MET471	4.9	35.9	1.0

Chlorine binding site 3 out of 4 in 8udf

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Chlorine Binding Sites List in 8udf

Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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:Cl702 b:69.9 occ:1.00	O	A:HOH1005	2.2	36.9	0.5
	O	A:HOH887	3.3	49.9	1.0
	N	A:LYS311	3.4	26.2	1.0
	NE	A:ARG310	3.5	40.9	1.0
	O	A:HOH811	3.7	44.2	1.0
	CB	A:LYS311	4.0	35.9	1.0
	CA	A:ARG310	4.1	27.9	1.0
	NH2	A:ARG310	4.2	50.9	1.0
	C	A:ARG310	4.3	24.2	1.0
	CZ	A:ARG310	4.3	51.3	1.0
	CA	A:LYS311	4.3	25.8	1.0
	CD	A:ARG310	4.3	42.4	1.0
	CB	A:ARG310	4.6	34.3	1.0
	O	A:PHE309	4.8	31.8	1.0
	CG	A:LYS311	5.0	41.0	1.0

Chlorine binding site 4 out of 4 in 8udf

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Chlorine Binding Sites List in 8udf

Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 3CL Protease with Inhibitor DEL_7

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 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:Cl703 b:62.4 occ:1.00	N	A:PHE409	3.3	23.1	1.0
	CA	A:LYS408	4.0	28.7	1.0
	CB	A:PHE409	4.1	21.8	1.0
	O	A:PHE409	4.1	29.0	1.0
	C	A:LYS408	4.1	23.2	1.0
	CA	A:PHE409	4.2	20.5	1.0
	CB	A:LYS408	4.4	34.0	1.0
	CG	A:PHE409	4.5	25.8	1.0
	C	A:PHE409	4.6	23.3	1.0
	O	A:HOH974	4.7	59.2	1.0
	O	A:HOH927	4.7	62.8	1.0
	O	A:HOH955	4.7	58.9	1.0
	CD2	A:PHE409	4.9	31.3	1.0
	CG	A:LYS408	5.0	41.9	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: Sun Jul 13 14:50:35 2025

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