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Fluorine in PDB 6w2a: 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J

Enzymatic activity of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J

All present enzymatic activity of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J, PDB code: 6w2a was solved by M.M.Kashipathy, S.Lovell, K.P.Battaile, A.D.Rathnayake, J.Zheng, Y.Kim, H.N.Nguyen, K.O.Chang, W.C.Groutas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.93 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.004, 99.999, 59.269, 90.00, 108.31, 90.00
R / Rfree (%) 17.2 / 20.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J (pdb code 6w2a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J, PDB code: 6w2a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6w2a

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Fluorine binding site 1 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:51.6
occ:0.50
 F01 A:VDJ401 0.0 51.6 0.5
F01 A:QYS402 0.0 51.6 0.5
C02 A:VDJ401 1.4 46.5 0.5
C02 A:QYS402 1.4 46.5 0.5
F03 A:VDJ401 2.1 48.2 0.5
F03 A:QYS402 2.1 48.2 0.5
C31 A:VDJ401 2.4 43.3 0.5
C31 A:QYS402 2.4 43.3 0.5
C04 A:VDJ401 2.4 42.9 0.5
C04 A:QYS402 2.4 42.9 0.5
C30 A:QYS402 3.7 38.7 0.5
C30 A:VDJ401 3.7 38.7 0.5
C05 A:QYS402 3.7 38.5 0.5
C05 A:VDJ401 3.7 38.5 0.5
CB A:ALA191 3.9 37.1 1.0
C06 A:QYS402 4.2 37.9 0.5
C06 A:VDJ401 4.2 37.9 0.5
CG A:PRO168 4.4 36.9 1.0
CA A:ALA191 4.4 29.5 1.0
CB A:PRO168 4.6 30.6 1.0
N A:ALA191 4.8 30.4 1.0
CA A:PRO168 4.9 27.0 1.0

Fluorine binding site 2 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 2 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:48.2
occ:0.50
 F03 A:VDJ401 0.0 48.2 0.5
F03 A:QYS402 0.0 48.2 0.5
C02 A:QYS402 1.3 46.5 0.5
C02 A:VDJ401 1.3 46.5 0.5
F01 A:QYS402 2.1 51.6 0.5
F01 A:VDJ401 2.1 51.6 0.5
C31 A:QYS402 2.4 43.3 0.5
C31 A:VDJ401 2.4 43.3 0.5
C04 A:VDJ401 2.4 42.9 0.5
C04 A:QYS402 2.4 42.9 0.5
C30 A:QYS402 2.9 38.7 0.5
C30 A:VDJ401 2.9 38.7 0.5
C05 A:VDJ401 3.0 38.5 0.5
C05 A:QYS402 3.0 38.5 0.5
CG A:PRO168 3.0 36.9 1.0
CD A:PRO168 3.2 26.0 1.0
N A:PRO168 3.5 25.7 1.0
C06 A:QYS402 3.6 37.9 0.5
C06 A:VDJ401 3.6 37.9 0.5
CB A:PRO168 3.6 30.6 1.0
CA A:PRO168 3.6 27.0 1.0
CB A:ALA191 3.6 37.1 1.0
CA A:ALA191 3.6 29.5 1.0
O A:HOH554 3.9 28.2 1.0
C A:LEU167 4.2 27.8 1.0
N A:ALA191 4.4 30.4 1.0
O A:THR190 4.7 29.7 1.0
C07 A:QYS402 4.7 34.1 0.5
C07 A:VDJ401 4.8 34.1 0.5
O A:LEU167 4.8 28.6 1.0
C A:ALA191 4.8 28.1 1.0
O A:GLU166 4.8 28.5 1.0
CA A:LEU167 4.8 21.4 1.0
C A:THR190 4.8 30.8 1.0
N A:GLN192 4.8 23.8 1.0

Fluorine binding site 3 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 3 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:51.6
occ:0.50
 F01 A:QYS402 0.0 51.6 0.5
F01 A:VDJ401 0.0 51.6 0.5
C02 A:VDJ401 1.4 46.5 0.5
C02 A:QYS402 1.4 46.5 0.5
F03 A:VDJ401 2.1 48.2 0.5
F03 A:QYS402 2.1 48.2 0.5
C31 A:VDJ401 2.4 43.3 0.5
C31 A:QYS402 2.4 43.3 0.5
C04 A:VDJ401 2.4 42.9 0.5
C04 A:QYS402 2.4 42.9 0.5
C30 A:QYS402 3.7 38.7 0.5
C30 A:VDJ401 3.7 38.7 0.5
C05 A:QYS402 3.7 38.5 0.5
C05 A:VDJ401 3.7 38.5 0.5
CB A:ALA191 3.9 37.1 1.0
C06 A:QYS402 4.2 37.9 0.5
C06 A:VDJ401 4.2 37.9 0.5
CG A:PRO168 4.4 36.9 1.0
CA A:ALA191 4.4 29.5 1.0
CB A:PRO168 4.6 30.6 1.0
N A:ALA191 4.8 30.4 1.0
CA A:PRO168 4.9 27.0 1.0

Fluorine binding site 4 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 4 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:48.2
occ:0.50
 F03 A:QYS402 0.0 48.2 0.5
F03 A:VDJ401 0.0 48.2 0.5
C02 A:QYS402 1.3 46.5 0.5
C02 A:VDJ401 1.3 46.5 0.5
F01 A:QYS402 2.1 51.6 0.5
F01 A:VDJ401 2.1 51.6 0.5
C31 A:QYS402 2.4 43.3 0.5
C31 A:VDJ401 2.4 43.3 0.5
C04 A:VDJ401 2.4 42.9 0.5
C04 A:QYS402 2.4 42.9 0.5
C30 A:QYS402 2.9 38.7 0.5
C30 A:VDJ401 2.9 38.7 0.5
C05 A:VDJ401 3.0 38.5 0.5
C05 A:QYS402 3.0 38.5 0.5
CG A:PRO168 3.0 36.9 1.0
CD A:PRO168 3.2 26.0 1.0
N A:PRO168 3.5 25.7 1.0
C06 A:QYS402 3.6 37.9 0.5
C06 A:VDJ401 3.6 37.9 0.5
CB A:PRO168 3.6 30.6 1.0
CB A:ALA191 3.6 37.1 1.0
CA A:PRO168 3.6 27.0 1.0
CA A:ALA191 3.6 29.5 1.0
O A:HOH554 3.9 28.2 1.0
C A:LEU167 4.2 27.8 1.0
N A:ALA191 4.4 30.4 1.0
O A:THR190 4.7 29.7 1.0
C07 A:QYS402 4.7 34.1 0.5
C07 A:VDJ401 4.8 34.1 0.5
C A:ALA191 4.8 28.1 1.0
O A:LEU167 4.8 28.6 1.0
O A:GLU166 4.8 28.5 1.0
CA A:LEU167 4.8 21.4 1.0
C A:THR190 4.8 30.8 1.0
N A:GLN192 4.8 23.8 1.0

Fluorine binding site 5 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 5 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:64.0
occ:0.50
 F01 B:QYS401 0.0 64.0 0.5
F01 B:VDJ402 0.0 64.0 0.5
C02 B:QYS401 1.4 58.5 0.5
C02 B:VDJ402 1.4 58.5 0.5
F03 B:VDJ402 2.1 63.5 0.5
F03 B:QYS401 2.1 63.5 0.5
C31 B:QYS401 2.4 56.8 0.5
C31 B:VDJ402 2.4 56.8 0.5
C04 B:QYS401 2.4 59.5 0.5
C04 B:VDJ402 2.4 59.5 0.5
C05 B:QYS401 3.1 48.9 0.5
C05 B:VDJ402 3.1 48.9 0.5
C30 B:QYS401 3.5 52.8 0.5
C30 B:VDJ402 3.5 52.8 0.5
C06 B:VDJ402 3.6 48.1 0.5
C06 B:QYS401 3.6 48.1 0.5
CB B:ALA191 4.4 53.8 1.0
CA B:ALA191 4.7 56.6 1.0
N B:ALA191 4.7 63.5 1.0

Fluorine binding site 6 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 6 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:63.5
occ:0.50
 F03 B:QYS401 0.0 63.5 0.5
F03 B:VDJ402 0.0 63.5 0.5
C02 B:QYS401 1.3 58.5 0.5
C02 B:VDJ402 1.3 58.5 0.5
F01 B:QYS401 2.1 64.0 0.5
F01 B:VDJ402 2.1 64.0 0.5
C31 B:VDJ402 2.4 56.8 0.5
C31 B:QYS401 2.4 56.8 0.5
C04 B:QYS401 2.4 59.5 0.5
C04 B:VDJ402 2.4 59.5 0.5
CG B:PRO168 3.3 46.3 1.0
CB B:ALA191 3.5 53.8 1.0
CB B:PRO168 3.5 39.2 1.0
C30 B:VDJ402 3.5 52.8 0.5
C30 B:QYS401 3.5 52.8 0.5
C05 B:QYS401 3.7 48.9 0.5
C05 B:VDJ402 3.7 48.9 0.5
CA B:PRO168 3.8 40.5 1.0
CA B:ALA191 3.8 56.6 1.0
CD B:PRO168 4.0 46.4 1.0
N B:PRO168 4.0 36.2 1.0
C06 B:VDJ402 4.2 48.1 0.5
C06 B:QYS401 4.2 48.1 0.5
N B:ALA191 4.5 63.5 1.0
O B:HOH588 4.5 39.5 1.0
C B:LEU167 4.8 33.5 1.0

Fluorine binding site 7 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 7 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:64.0
occ:0.50
 F01 B:VDJ402 0.0 64.0 0.5
F01 B:QYS401 0.0 64.0 0.5
C02 B:QYS401 1.4 58.5 0.5
C02 B:VDJ402 1.4 58.5 0.5
F03 B:VDJ402 2.1 63.5 0.5
F03 B:QYS401 2.1 63.5 0.5
C31 B:QYS401 2.4 56.8 0.5
C31 B:VDJ402 2.4 56.8 0.5
C04 B:QYS401 2.4 59.5 0.5
C04 B:VDJ402 2.4 59.5 0.5
C05 B:QYS401 3.0 48.9 0.5
C05 B:VDJ402 3.1 48.9 0.5
C30 B:QYS401 3.4 52.8 0.5
C30 B:VDJ402 3.5 52.8 0.5
C06 B:VDJ402 3.5 48.1 0.5
C06 B:QYS401 3.5 48.1 0.5
CB B:ALA191 4.5 53.8 1.0
CA B:ALA191 4.7 56.6 1.0
N B:ALA191 4.7 63.5 1.0

Fluorine binding site 8 out of 8 in 6w2a

Go back to Fluorine Binding Sites List in 6w2a
Fluorine binding site 8 out of 8 in the 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 1.65 A Resolution Structure of Sars-Cov 3CL Protease in Complex with Inhibitor 7J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:63.5
occ:0.50
 F03 B:VDJ402 0.0 63.5 0.5
F03 B:QYS401 0.0 63.5 0.5
C02 B:QYS401 1.3 58.5 0.5
C02 B:VDJ402 1.3 58.5 0.5
F01 B:QYS401 2.1 64.0 0.5
F01 B:VDJ402 2.1 64.0 0.5
C31 B:VDJ402 2.4 56.8 0.5
C04 B:QYS401 2.4 59.5 0.5
C04 B:VDJ402 2.4 59.5 0.5
C31 B:QYS401 2.4 56.8 0.5
CG B:PRO168 3.3 46.3 1.0
CB B:ALA191 3.4 53.8 1.0
C30 B:VDJ402 3.5 52.8 0.5
C30 B:QYS401 3.5 52.8 0.5
CB B:PRO168 3.5 39.2 1.0
C05 B:QYS401 3.7 48.9 0.5
C05 B:VDJ402 3.7 48.9 0.5
CA B:ALA191 3.8 56.6 1.0
CA B:PRO168 3.8 40.5 1.0
CD B:PRO168 4.1 46.4 1.0
N B:PRO168 4.1 36.2 1.0
C06 B:VDJ402 4.2 48.1 0.5
C06 B:QYS401 4.2 48.1 0.5
N B:ALA191 4.5 63.5 1.0
O B:HOH588 4.6 39.5 1.0
C B:LEU167 4.8 33.5 1.0

Reference:

A.D.Rathnayake, J.Zheng, Y.Kim, K.D.Perera, S.Mackin, D.K.Meyerholz, M.M.Kashipathy, K.P.Battaile, S.Lovell, S.Perlman, W.C.Groutas, K.O.Chang. 3C-Like Protease Inhibitors Block Coronavirus Replication in Vitro and Improve Survival in Mers-Cov-Infected Mice. Sci Transl Med V. 12 2020.
ISSN: ESSN 1946-6242
PubMed: 32747425
DOI: 10.1126/SCITRANSLMED.ABC5332
Page generated: Tue Jul 15 17:00:22 2025

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