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Fluorine in PDB 7vu6: The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3

Enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3

All present enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3:
3.4.22.69;

Protein crystallography data

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3, PDB code: 7vu6 was solved by S.Yamamoto, J.Yamane, Y.Tachibana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.99 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.468, 99.229, 58.883, 90, 108.05, 90
R / Rfree (%) 22.4 / 27.9

Other elements in 7vu6:

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

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 (pdb code 7vu6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3, PDB code: 7vu6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 1 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:15.2
occ:1.00
 F28 A:7YY501 0.0 15.2 1.0
C27 A:7YY501 1.2 15.0 1.0
C26 A:7YY501 2.3 13.6 1.0
C29 A:7YY501 2.3 14.0 1.0
C25 A:7YY501 2.7 14.3 1.0
O A:HOH737 3.1 25.2 1.0
CB A:GLN189 3.3 24.9 1.0
CA A:GLN189 3.4 21.9 1.0
CG A:GLN189 3.4 26.2 1.0
C34 A:7YY501 3.5 13.8 1.0
C30 A:7YY501 3.6 14.2 1.0
O A:HOH638 3.6 22.8 1.0
NE2 A:GLN189 3.7 31.4 1.0
CD A:GLN189 3.9 28.7 1.0
N A:GLN189 3.9 21.3 1.0
C32 A:7YY501 4.1 13.7 1.0
N24 A:7YY501 4.1 13.7 1.0
O A:ARG188 4.1 17.4 1.0
C A:ARG188 4.3 18.6 1.0
NE2 A:HIS41 4.5 13.2 1.0
CB A:MET165 4.5 12.9 1.0
F31 A:7YY501 4.6 17.9 1.0
C A:GLN189 4.6 23.4 1.0
O36 A:7YY501 4.7 13.3 1.0
OE1 A:GLN189 4.9 28.9 1.0
SD A:MET165 4.9 16.3 1.0
C35 A:7YY501 4.9 12.6 1.0
CE1 A:HIS41 5.0 13.7 1.0

Fluorine binding site 2 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 2 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:17.9
occ:1.00
 F31 A:7YY501 0.0 17.9 1.0
C30 A:7YY501 1.2 14.2 1.0
C29 A:7YY501 2.3 14.0 1.0
C32 A:7YY501 2.3 13.7 1.0
F33 A:7YY501 2.6 12.3 1.0
CA A:ASP187 3.0 13.7 1.0
CB A:ASP187 3.1 12.8 1.0
C A:ASP187 3.1 14.0 1.0
C34 A:7YY501 3.5 13.8 1.0
C27 A:7YY501 3.5 15.0 1.0
N A:ARG188 3.6 16.1 1.0
O A:ASP187 3.6 14.0 1.0
ND1 A:HIS41 3.6 12.2 1.0
CG A:HIS41 3.8 12.2 1.0
CE1 A:HIS41 3.9 13.7 1.0
SD A:MET165 3.9 16.3 1.0
C26 A:7YY501 4.0 13.6 1.0
CD2 A:HIS41 4.1 12.0 1.0
NE2 A:HIS41 4.1 13.2 1.0
CB A:HIS41 4.3 12.9 1.0
N A:ASP187 4.4 12.9 1.0
O A:HOH678 4.4 10.1 1.0
CA A:ARG188 4.5 19.6 1.0
OH A:TYR54 4.5 14.4 1.0
O A:VAL186 4.5 15.0 1.0
CG A:ASP187 4.5 12.4 1.0
C A:ARG188 4.5 18.6 1.0
F28 A:7YY501 4.6 15.2 1.0
CD2 A:HIS164 4.6 9.0 1.0
CB A:HIS164 4.7 8.8 1.0
O A:ARG188 4.7 17.4 1.0
CB A:MET165 4.7 12.9 1.0
C A:VAL186 4.9 13.7 1.0
CG A:MET165 4.9 13.9 1.0

Fluorine binding site 3 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 3 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:12.3
occ:1.00
 F33 A:7YY501 0.0 12.3 1.0
C32 A:7YY501 1.2 13.7 1.0
C34 A:7YY501 2.3 13.8 1.0
C30 A:7YY501 2.3 14.2 1.0
F31 A:7YY501 2.6 17.9 1.0
O A:HIS164 3.3 10.5 1.0
CG A:HIS41 3.5 12.2 1.0
C26 A:7YY501 3.5 13.6 1.0
C29 A:7YY501 3.5 14.0 1.0
CB A:HIS41 3.5 12.9 1.0
CD2 A:HIS41 3.6 12.0 1.0
SG A:CYS145 3.6 12.5 1.0
CB A:HIS164 3.7 8.8 1.0
C A:HIS164 3.7 9.6 1.0
CA A:HIS164 3.9 9.2 1.0
CD2 A:HIS164 3.9 9.0 1.0
C27 A:7YY501 4.0 15.0 1.0
CG A:HIS164 4.1 9.3 1.0
O A:HOH678 4.2 10.1 1.0
ND1 A:HIS41 4.3 12.2 1.0
NE2 A:HIS41 4.4 13.2 1.0
CL2 A:7YY501 4.5 13.8 1.0
CB A:MET165 4.6 12.9 1.0
N A:MET165 4.7 9.9 1.0
CE1 A:HIS41 4.7 13.7 1.0
C25 A:7YY501 4.8 14.3 1.0
N24 A:7YY501 4.9 13.7 1.0
CB A:ASP187 4.9 12.8 1.0
CB A:PRO39 5.0 11.0 1.0

Fluorine binding site 4 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 4 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.4
occ:1.00
 F28 B:7YY501 0.0 16.4 1.0
C27 B:7YY501 1.3 15.4 1.0
C26 B:7YY501 2.3 14.3 1.0
C29 B:7YY501 2.3 14.7 1.0
C25 B:7YY501 2.8 13.9 1.0
O B:HOH688 3.2 30.0 1.0
CG B:GLN189 3.2 24.1 1.0
CB B:GLN189 3.2 21.6 1.0
CA B:GLN189 3.3 21.8 1.0
C34 B:7YY501 3.5 14.0 1.0
O B:HOH741 3.5 39.3 1.0
C30 B:7YY501 3.6 14.6 1.0
O B:HOH677 3.6 12.8 1.0
CD B:GLN189 3.8 26.5 1.0
OE1 B:GLN189 3.9 33.4 1.0
N B:GLN189 3.9 21.1 1.0
C32 B:7YY501 4.1 14.6 1.0
N24 B:7YY501 4.1 13.8 1.0
O B:ARG188 4.2 18.2 1.0
C B:ARG188 4.3 18.2 1.0
CB B:MET165 4.4 15.5 1.0
NE2 B:HIS41 4.5 13.4 1.0
C B:GLN189 4.5 25.0 1.0
O36 B:7YY501 4.6 13.8 1.0
F31 B:7YY501 4.6 16.7 1.0
SD B:MET165 4.8 16.6 1.0
NE2 B:GLN189 4.8 25.4 1.0
CE1 B:HIS41 4.9 13.5 1.0
N B:THR190 4.9 29.1 1.0
C35 B:7YY501 4.9 13.1 1.0

Fluorine binding site 5 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 5 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.7
occ:1.00
 F31 B:7YY501 0.0 16.7 1.0
C30 B:7YY501 1.3 14.6 1.0
C29 B:7YY501 2.3 14.7 1.0
C32 B:7YY501 2.4 14.6 1.0
F33 B:7YY501 2.7 12.7 1.0
CB B:ASP187 2.9 13.7 1.0
CA B:ASP187 3.0 14.8 1.0
C B:ASP187 3.1 16.0 1.0
O B:ASP187 3.4 16.1 1.0
ND1 B:HIS41 3.5 13.5 1.0
C34 B:7YY501 3.6 14.0 1.0
C27 B:7YY501 3.6 15.4 1.0
N B:ARG188 3.6 17.2 1.0
CG B:HIS41 3.7 12.2 1.0
CE1 B:HIS41 3.9 13.5 1.0
SD B:MET165 4.0 16.6 1.0
CB B:HIS41 4.1 11.8 1.0
C26 B:7YY501 4.1 14.3 1.0
CD2 B:HIS41 4.2 12.6 1.0
O B:HOH672 4.2 14.0 1.0
CG B:ASP187 4.3 13.8 1.0
NE2 B:HIS41 4.3 13.4 1.0
N B:ASP187 4.4 13.9 1.0
OH B:TYR54 4.5 16.8 1.0
CD2 B:HIS164 4.5 10.3 1.0
CB B:HIS164 4.6 10.8 1.0
CA B:ARG188 4.6 19.6 1.0
F28 B:7YY501 4.6 16.4 1.0
O B:VAL186 4.7 13.2 1.0
C B:ARG188 4.7 18.2 1.0
OD2 B:ASP187 4.8 15.0 1.0
O B:ARG188 4.8 18.2 1.0
CB B:MET165 4.8 15.5 1.0
CG B:HIS164 4.9 10.6 1.0
CG B:MET165 5.0 16.4 1.0

Fluorine binding site 6 out of 6 in 7vu6

Go back to Fluorine Binding Sites List in 7vu6
Fluorine binding site 6 out of 6 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:12.7
occ:1.00
 F33 B:7YY501 0.0 12.7 1.0
C32 B:7YY501 1.2 14.6 1.0
C34 B:7YY501 2.3 14.0 1.0
C30 B:7YY501 2.3 14.6 1.0
F31 B:7YY501 2.7 16.7 1.0
O B:HIS164 3.3 10.9 1.0
CB B:HIS41 3.3 11.8 1.0
CG B:HIS41 3.4 12.2 1.0
C29 B:7YY501 3.5 14.7 1.0
SG B:CYS145 3.5 12.0 1.0
CD2 B:HIS41 3.5 12.6 1.0
C26 B:7YY501 3.6 14.3 1.0
CB B:HIS164 3.8 10.8 1.0
C B:HIS164 3.8 11.8 1.0
CA B:HIS164 3.9 10.3 1.0
CD2 B:HIS164 4.0 10.3 1.0
C27 B:7YY501 4.0 15.4 1.0
CG B:HIS164 4.2 10.6 1.0
ND1 B:HIS41 4.2 13.5 1.0
O B:HOH672 4.2 14.0 1.0
NE2 B:HIS41 4.3 13.4 1.0
CL2 B:7YY501 4.4 14.2 1.0
CE1 B:HIS41 4.7 13.5 1.0
CB B:MET165 4.7 15.5 1.0
CB B:PRO39 4.8 8.9 1.0
N B:MET165 4.8 13.1 1.0
C25 B:7YY501 4.9 13.9 1.0
CA B:HIS41 4.9 11.3 1.0
CB B:ASP187 4.9 13.7 1.0
N24 B:7YY501 5.0 13.8 1.0

Reference:

Y.Unoh, S.Uehara, K.Nakahara, H.Nobori, Y.Yamatsu, S.Yamamoto, Y.Maruyama, Y.Taoda, K.Kasamatsu, T.Suto, K.Kouki, A.Nakahashi, S.Kawashima, T.Sanaki, S.Toba, K.Uemura, T.Mizutare, S.Ando, M.Sasaki, Y.Orba, H.Sawa, A.Sato, T.Sato, T.Kato, Y.Tachibana. Discovery of S-217622, A Noncovalent Oral Sars-Cov-2 3CL Protease Inhibitor Clinical Candidate For Treating Covid-19. J.Med.Chem. V. 65 6499 2022.
ISSN: ISSN 0022-2623
PubMed: 35352927
DOI: 10.1021/ACS.JMEDCHEM.2C00117
Page generated: Fri Aug 2 14:39:02 2024

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