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Fluorine in PDB 7vth: The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1

Enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1

All present enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1:
3.4.22.69;

Protein crystallography data

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1, PDB code: 7vth was solved by S.Yamamoto, Y.Tachibana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.95 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.411, 54.27, 114.497, 90, 99.42, 90
R / Rfree (%) 20.5 / 25.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1 (pdb code 7vth). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1, PDB code: 7vth:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 7vth

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Fluorine binding site 1 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:42.3
occ:1.00
 F19 A:7XB501 0.0 42.3 1.0
C18 A:7XB501 1.4 46.0 1.0
O17 A:7XB501 2.3 42.7 1.0
F20 A:7XB501 2.3 51.4 1.0
C16 A:7XB501 3.0 36.6 1.0
C21 A:7XB501 3.3 34.8 1.0
C15 A:7XB501 4.2 38.2 1.0
CG2 A:THR26 4.2 29.8 1.0
O A:HOH638 4.6 22.1 1.0
O A:THR26 4.6 23.9 1.0
C22 A:7XB501 4.6 33.6 1.0
N A:THR26 4.7 30.1 1.0
O A:THR24 4.7 40.2 1.0

Fluorine binding site 2 out of 10 in 7vth

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Fluorine binding site 2 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:51.4
occ:1.00
 F20 A:7XB501 0.0 51.4 1.0
C18 A:7XB501 1.4 46.0 1.0
O17 A:7XB501 2.3 42.7 1.0
F19 A:7XB501 2.3 42.3 1.0
O A:THR24 2.5 40.2 1.0
CA A:THR25 3.3 33.1 1.0
C A:THR24 3.5 37.4 1.0
N A:THR26 3.5 30.1 1.0
C16 A:7XB501 3.5 36.6 1.0
N A:THR25 3.8 36.4 1.0
C A:THR25 3.9 31.1 1.0
C21 A:7XB501 4.1 34.8 1.0
CG2 A:THR26 4.3 29.8 1.0
CB A:THR25 4.4 34.2 1.0
C15 A:7XB501 4.6 38.2 1.0
CG2 A:THR25 4.6 34.2 1.0
CA A:THR26 4.7 28.5 1.0
OG1 A:THR25 4.7 35.3 1.0
CB A:THR26 4.8 30.4 1.0
O A:THR26 4.8 23.9 1.0
CA A:THR24 4.8 35.8 1.0

Fluorine binding site 3 out of 10 in 7vth

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Fluorine binding site 3 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.2
occ:1.00
 F28 A:7XB501 0.0 35.2 1.0
C27 A:7XB501 1.4 33.4 1.0
C26 A:7XB501 2.4 30.6 1.0
C29 A:7XB501 2.4 31.4 1.0
F30 A:7XB501 2.7 33.0 1.0
C A:ARG188 2.8 19.1 1.0
O A:ARG188 3.0 16.0 1.0
N A:GLN189 3.1 22.1 1.0
CA A:ARG188 3.2 18.6 1.0
N A:ARG188 3.2 18.0 1.0
C25 A:7XB501 3.6 29.3 1.0
CA A:GLN189 3.6 25.0 1.0
C31 A:7XB501 3.7 29.8 1.0
C A:ASP187 3.8 17.2 1.0
CE A:MET165 4.0 39.9 1.0
SD A:MET165 4.1 39.3 1.0
CB A:GLN189 4.1 25.0 1.0
C33 A:7XB501 4.1 29.9 1.0
CE1 A:HIS41 4.3 30.6 1.0
CA A:ASP187 4.3 16.4 1.0
O A:ASP187 4.4 15.5 1.0
OE1 A:GLN189 4.5 28.7 1.0
NE2 A:HIS41 4.5 29.2 1.0
O A:MET49 4.7 31.5 1.0
ND1 A:HIS41 4.7 30.1 1.0
CB A:ARG188 4.7 19.7 1.0
CB A:MET165 4.8 25.6 1.0
F32 A:7XB501 4.8 30.7 1.0
C24 A:7XB501 4.8 28.2 1.0
CD A:GLN189 4.9 26.2 1.0
O A:VAL186 4.9 15.0 1.0

Fluorine binding site 4 out of 10 in 7vth

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Fluorine binding site 4 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:33.0
occ:1.00
 F30 A:7XB501 0.0 33.0 1.0
C29 A:7XB501 1.4 31.4 1.0
C27 A:7XB501 2.3 33.4 1.0
C31 A:7XB501 2.4 29.8 1.0
F28 A:7XB501 2.7 35.2 1.0
F32 A:7XB501 2.8 30.7 1.0
CE A:MET165 3.0 39.9 1.0
CB A:ASP187 3.1 15.8 1.0
CA A:ASP187 3.1 16.4 1.0
C A:ASP187 3.2 17.2 1.0
N A:ARG188 3.6 18.0 1.0
O A:ASP187 3.6 15.5 1.0
C26 A:7XB501 3.6 30.6 1.0
C33 A:7XB501 3.6 29.9 1.0
ND1 A:HIS41 3.7 30.1 1.0
CG A:HIS41 3.8 26.9 1.0
CE1 A:HIS41 4.1 30.6 1.0
C25 A:7XB501 4.1 29.3 1.0
CB A:HIS41 4.1 23.7 1.0
CD2 A:HIS41 4.2 28.3 1.0
SD A:MET165 4.3 39.3 1.0
CG A:ASP187 4.4 16.4 1.0
CA A:ARG188 4.4 18.6 1.0
O A:HOH646 4.4 10.9 1.0
NE2 A:HIS41 4.4 29.2 1.0
OH A:TYR54 4.4 18.4 1.0
N A:ASP187 4.5 15.6 1.0
CB A:MET165 4.8 25.6 1.0
OD2 A:ASP187 4.8 16.6 1.0
C A:ARG188 4.8 19.1 1.0
O A:VAL186 4.9 15.0 1.0
CB A:HIS164 4.9 14.4 1.0

Fluorine binding site 5 out of 10 in 7vth

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Fluorine binding site 5 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:30.7
occ:1.00
 F32 A:7XB501 0.0 30.7 1.0
C31 A:7XB501 1.4 29.8 1.0
C33 A:7XB501 2.4 29.9 1.0
C29 A:7XB501 2.4 31.4 1.0
F30 A:7XB501 2.8 33.0 1.0
O A:HIS164 3.2 20.1 1.0
CB A:HIS41 3.3 23.7 1.0
CG A:HIS41 3.4 26.9 1.0
CD2 A:HIS41 3.6 28.3 1.0
SG A:CYS145 3.6 14.1 0.5
C27 A:7XB501 3.7 33.4 1.0
C25 A:7XB501 3.7 29.3 1.0
C A:HIS164 3.7 17.3 1.0
CB A:HIS164 3.8 14.4 1.0
CA A:HIS164 4.0 15.4 1.0
O A:HOH646 4.0 10.9 1.0
SG A:CYS145 4.2 22.6 0.5
C26 A:7XB501 4.2 30.6 1.0
ND1 A:HIS41 4.3 30.1 1.0
CD2 A:HIS164 4.3 13.8 1.0
CG A:HIS164 4.4 14.5 1.0
CE A:MET165 4.4 39.9 1.0
NE2 A:HIS41 4.5 29.2 1.0
CB A:MET165 4.7 25.6 1.0
N A:MET165 4.7 18.6 1.0
C14 A:7XB501 4.7 38.2 1.0
CA A:HIS41 4.8 21.9 1.0
F28 A:7XB501 4.8 35.2 1.0
CE1 A:HIS41 4.8 30.6 1.0
CB A:ASP187 4.9 15.8 1.0
N23 A:7XB501 5.0 27.0 1.0
CA A:MET165 5.0 20.9 1.0

Fluorine binding site 6 out of 10 in 7vth

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Fluorine binding site 6 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:38.3
occ:1.00
 F19 B:7XB401 0.0 38.3 1.0
C18 B:7XB401 1.4 34.1 1.0
F20 B:7XB401 2.2 37.7 1.0
O17 B:7XB401 2.3 30.2 1.0
C16 B:7XB401 2.7 25.8 1.0
C21 B:7XB401 3.0 23.3 1.0
C15 B:7XB401 3.7 24.0 1.0
C22 B:7XB401 4.1 22.6 1.0
ND2 B:ASN142 4.2 33.2 1.0
O B:THR26 4.4 11.0 1.0
CG2 B:THR26 4.4 19.9 1.0
N B:THR26 4.6 14.6 1.0
C13 B:7XB401 4.6 24.0 1.0
O B:THR24 4.8 20.1 1.0
C12 B:7XB401 4.8 22.5 1.0

Fluorine binding site 7 out of 10 in 7vth

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Fluorine binding site 7 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.7
occ:1.00
 F20 B:7XB401 0.0 37.7 1.0
C18 B:7XB401 1.4 34.1 1.0
F19 B:7XB401 2.2 38.3 1.0
O17 B:7XB401 2.3 30.2 1.0
O B:THR24 2.7 20.1 1.0
N B:THR26 3.4 14.6 1.0
CG2 B:THR26 3.6 19.9 1.0
C16 B:7XB401 3.6 25.8 1.0
CA B:THR25 3.8 15.6 1.0
C B:THR24 3.8 18.4 1.0
C B:THR25 4.0 15.1 1.0
C21 B:7XB401 4.2 23.3 1.0
CB B:THR26 4.2 17.7 1.0
CA B:THR26 4.3 14.8 1.0
N B:THR25 4.3 16.9 1.0
O B:THR26 4.5 11.0 1.0
C15 B:7XB401 4.6 24.0 1.0
C B:THR26 4.9 13.0 1.0

Fluorine binding site 8 out of 10 in 7vth

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Fluorine binding site 8 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:30.4
occ:1.00
 F28 B:7XB401 0.0 30.4 1.0
C27 B:7XB401 1.4 28.0 1.0
C26 B:7XB401 2.4 25.8 1.0
C29 B:7XB401 2.4 28.2 1.0
F30 B:7XB401 2.8 33.9 1.0
N B:ARG188 3.4 15.0 1.0
O B:HOH626 3.4 21.6 1.0
C B:ARG188 3.6 18.8 1.0
C25 B:7XB401 3.6 23.7 1.0
O B:ARG188 3.6 18.2 1.0
CA B:ARG188 3.7 17.5 1.0
C31 B:7XB401 3.7 26.3 1.0
C B:ASP187 3.7 13.0 1.0
NE2 B:HIS41 3.9 15.4 1.0
C33 B:7XB401 4.1 24.2 1.0
CA B:ASP187 4.2 11.0 1.0
N B:GLN189 4.2 18.5 1.0
O B:ASP187 4.2 14.5 1.0
CE1 B:HIS41 4.4 15.2 1.0
CE B:MET165 4.4 29.8 1.0
SD B:MET165 4.4 30.4 1.0
CD2 B:HIS41 4.4 15.2 1.0
O B:MET49 4.7 30.2 1.0
F32 B:7XB401 4.8 24.4 1.0
O B:VAL186 4.8 9.2 1.0
C24 B:7XB401 4.9 21.9 1.0
CB B:MET165 4.9 18.0 1.0
CB B:ASP187 5.0 9.8 1.0

Fluorine binding site 9 out of 10 in 7vth

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Fluorine binding site 9 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.9
occ:1.00
 F30 B:7XB401 0.0 33.9 1.0
C29 B:7XB401 1.4 28.2 1.0
C31 B:7XB401 2.4 26.3 1.0
C27 B:7XB401 2.4 28.0 1.0
F32 B:7XB401 2.7 24.4 1.0
F28 B:7XB401 2.8 30.4 1.0
CB B:ASP187 3.0 9.8 1.0
CA B:ASP187 3.2 11.0 1.0
CD2 B:HIS41 3.4 15.2 1.0
C B:ASP187 3.4 13.0 1.0
CE B:MET165 3.5 29.8 1.0
C33 B:7XB401 3.6 24.2 1.0
C26 B:7XB401 3.6 25.8 1.0
CG B:HIS41 3.7 14.1 1.0
O B:ASP187 3.7 14.5 1.0
NE2 B:HIS41 3.8 15.4 1.0
N B:ARG188 4.0 15.0 1.0
C25 B:7XB401 4.1 23.7 1.0
ND1 B:HIS41 4.2 15.6 1.0
CB B:HIS41 4.2 12.5 1.0
CE1 B:HIS41 4.2 15.2 1.0
O B:HOH595 4.3 8.2 1.0
OH B:TYR54 4.3 9.9 1.0
CG B:ASP187 4.4 9.1 1.0
SD B:MET165 4.6 30.4 1.0
N B:ASP187 4.6 10.0 1.0
CB B:MET165 4.8 18.0 1.0
OD2 B:ASP187 4.9 8.6 1.0
CB B:HIS164 4.9 9.4 1.0
O B:VAL186 4.9 9.2 1.0
CA B:ARG188 4.9 17.5 1.0

Fluorine binding site 10 out of 10 in 7vth

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Fluorine binding site 10 out of 10 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:24.4
occ:1.00
 F32 B:7XB401 0.0 24.4 1.0
C31 B:7XB401 1.4 26.3 1.0
C29 B:7XB401 2.4 28.2 1.0
C33 B:7XB401 2.4 24.2 1.0
F30 B:7XB401 2.7 33.9 1.0
O B:HIS164 3.3 11.1 1.0
CB B:HIS41 3.5 12.5 1.0
CG B:HIS41 3.5 14.1 1.0
ND1 B:HIS41 3.6 15.6 1.0
C27 B:7XB401 3.6 28.0 1.0
SG B:CYS145 3.7 10.3 0.5
C25 B:7XB401 3.7 23.7 1.0
C B:HIS164 3.7 10.6 1.0
CB B:HIS164 3.8 9.4 1.0
SG B:CYS145 3.8 15.0 0.5
CA B:HIS164 3.9 9.6 1.0
O B:HOH595 4.1 8.2 1.0
C26 B:7XB401 4.2 25.8 1.0
CD2 B:HIS41 4.2 15.2 1.0
CD2 B:HIS164 4.3 9.4 1.0
CG B:HIS164 4.3 9.6 1.0
CE1 B:HIS41 4.3 15.2 1.0
CE B:MET165 4.6 29.8 1.0
NE2 B:HIS41 4.7 15.4 1.0
N B:MET165 4.7 12.3 1.0
CB B:MET165 4.7 18.0 1.0
F28 B:7XB401 4.8 30.4 1.0
C14 B:7XB401 4.9 25.2 1.0
CB B:ASP187 4.9 9.8 1.0
CA B:HIS41 5.0 10.9 1.0
CB B:PRO39 5.0 7.5 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: Wed Jul 16 01:20:20 2025

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