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Fluorine in PDB 7maz: Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

Enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139

All present enzymatic activity of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139:
3.4.22.69;

Protein crystallography data

The structure of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139, PDB code: 7maz was solved by G.J.Lockbaum, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.823, 105.273, 52.894, 90, 104.05, 90
R / Rfree (%) 16.4 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 (pdb code 7maz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139, PDB code: 7maz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7maz

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Fluorine binding site 1 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:0.61
 F30 A:YVD401 0.0 35.5 0.6
F30 A:YVD401 0.2 35.1 0.4
C24 A:YVD401 1.3 28.3 0.6
C24 A:YVD401 1.4 28.2 0.4
C29 A:YVD401 2.4 29.5 0.4
C25 A:YVD401 2.4 28.7 0.6
C29 A:YVD401 2.5 29.9 0.6
C25 A:YVD401 2.5 28.4 0.4
H291 A:YVD401 2.6 35.5 0.4
H251 A:YVD401 2.6 34.5 0.6
HA A:ASP187 2.6 22.4 1.0
H291 A:YVD401 2.7 35.9 0.6
H251 A:YVD401 2.8 34.1 0.4
N A:ARG188 2.8 21.9 1.0
C A:ASP187 2.8 21.7 1.0
C A:ARG188 2.9 22.8 1.0
O A:ARG188 3.0 21.4 1.0
H A:ARG188 3.1 26.3 1.0
CA A:ASP187 3.2 18.7 1.0
CA A:ARG188 3.2 30.0 1.0
HA A:ARG188 3.3 36.0 1.0
H391 A:YVD401 3.3 25.3 0.4
O A:ASP187 3.3 19.1 1.0
H391 A:YVD401 3.3 24.7 0.6
N A:GLN189 3.4 19.9 1.0
HA A:GLN189 3.5 28.1 1.0
O A:VAL186 3.8 20.2 1.0
C26 A:YVD401 3.8 25.4 0.6
C28 A:YVD401 3.8 26.8 0.4
C28 A:YVD401 3.8 27.0 0.6
HB2 A:ASP187 3.8 27.3 1.0
H A:GLN189 3.9 23.9 1.0
H381 A:YVD401 3.9 23.9 0.4
C26 A:YVD401 3.9 25.3 0.4
CA A:GLN189 3.9 23.4 1.0
HB2 A:GLN189 3.9 25.7 1.0
H381 A:YVD401 4.0 23.6 0.6
C39 A:YVD401 4.0 21.1 0.4
C39 A:YVD401 4.1 20.5 0.6
CB A:ASP187 4.1 22.8 1.0
HE22 A:GLN192 4.1 27.5 1.0
C27 A:YVD401 4.3 21.4 0.6
N A:ASP187 4.3 16.3 1.0
C27 A:YVD401 4.3 21.5 0.4
C38 A:YVD401 4.3 19.9 0.4
C38 A:YVD401 4.4 19.7 0.6
SD A:MET165 4.4 25.9 1.0
CB A:GLN189 4.4 21.4 1.0
C A:VAL186 4.5 16.9 1.0
HB3 A:ASP187 4.5 27.3 1.0
H281 A:YVD401 4.5 32.2 0.4
H261 A:YVD401 4.5 30.4 0.6
H281 A:YVD401 4.6 32.5 0.6
HE21 A:GLN192 4.6 27.5 1.0
HG3 A:GLN189 4.6 22.7 1.0
H261 A:YVD401 4.7 30.4 0.4
NE2 A:GLN192 4.7 22.9 1.0
CB A:ARG188 4.7 26.2 1.0
HH A:TYR54 4.8 31.5 1.0
HB2 A:ARG188 5.0 31.4 1.0
H A:ASP187 5.0 19.6 1.0

Fluorine binding site 2 out of 6 in 7maz

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Fluorine binding site 2 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.1
occ:0.39
 F30 A:YVD401 0.0 35.1 0.4
F30 A:YVD401 0.2 35.5 0.6
C24 A:YVD401 1.3 28.3 0.6
C24 A:YVD401 1.3 28.2 0.4
C25 A:YVD401 2.3 28.7 0.6
C25 A:YVD401 2.4 28.4 0.4
C29 A:YVD401 2.4 29.5 0.4
H251 A:YVD401 2.5 34.5 0.6
C29 A:YVD401 2.5 29.9 0.6
H251 A:YVD401 2.6 34.1 0.4
H291 A:YVD401 2.7 35.5 0.4
HA A:ASP187 2.8 22.4 1.0
H291 A:YVD401 2.8 35.9 0.6
N A:ARG188 2.8 21.9 1.0
C A:ASP187 2.8 21.7 1.0
C A:ARG188 2.9 22.8 1.0
O A:ARG188 3.0 21.4 1.0
H A:ARG188 3.1 26.3 1.0
CA A:ARG188 3.2 30.0 1.0
HA A:ARG188 3.2 36.0 1.0
O A:ASP187 3.3 19.1 1.0
CA A:ASP187 3.3 18.7 1.0
N A:GLN189 3.3 19.9 1.0
H391 A:YVD401 3.4 25.3 0.4
H391 A:YVD401 3.5 24.7 0.6
HA A:GLN189 3.5 28.1 1.0
C26 A:YVD401 3.7 25.4 0.6
H A:GLN189 3.8 23.9 1.0
C26 A:YVD401 3.8 25.3 0.4
C28 A:YVD401 3.8 26.8 0.4
C28 A:YVD401 3.8 27.0 0.6
HB2 A:GLN189 3.8 25.7 1.0
HB2 A:ASP187 3.8 27.3 1.0
CA A:GLN189 3.9 23.4 1.0
H381 A:YVD401 3.9 23.9 0.4
O A:VAL186 3.9 20.2 1.0
H381 A:YVD401 4.0 23.6 0.6
C39 A:YVD401 4.1 21.1 0.4
CB A:ASP187 4.2 22.8 1.0
C39 A:YVD401 4.2 20.5 0.6
C27 A:YVD401 4.2 21.4 0.6
C27 A:YVD401 4.3 21.5 0.4
HE22 A:GLN192 4.3 27.5 1.0
CB A:GLN189 4.3 21.4 1.0
C38 A:YVD401 4.4 19.9 0.4
N A:ASP187 4.4 16.3 1.0
H261 A:YVD401 4.4 30.4 0.6
C38 A:YVD401 4.4 19.7 0.6
H261 A:YVD401 4.5 30.4 0.4
H281 A:YVD401 4.6 32.2 0.4
HG3 A:GLN189 4.6 22.7 1.0
H281 A:YVD401 4.6 32.5 0.6
SD A:MET165 4.6 25.9 1.0
C A:VAL186 4.6 16.9 1.0
HB3 A:ASP187 4.6 27.3 1.0
HE21 A:GLN192 4.7 27.5 1.0
CB A:ARG188 4.7 26.2 1.0
HH A:TYR54 4.7 31.5 1.0
NE2 A:GLN192 4.8 22.9 1.0
HB2 A:ARG188 5.0 31.4 1.0
O A:MET49 5.0 29.6 1.0

Fluorine binding site 3 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 3 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:28.3
occ:0.61
 F40 A:YVD401 0.0 28.3 0.6
F40 A:YVD401 0.0 25.9 0.4
C34 A:YVD401 1.3 21.9 0.4
C34 A:YVD401 1.3 22.1 0.6
C35 A:YVD401 2.4 21.5 0.4
C35 A:YVD401 2.5 21.6 0.6
C39 A:YVD401 2.5 20.5 0.6
C39 A:YVD401 2.5 21.1 0.4
HB2 A:GLN192 2.6 21.6 1.0
H351 A:YVD401 2.6 25.8 0.4
H351 A:YVD401 2.7 25.9 0.6
HE3 A:MET165 2.7 31.6 1.0
H391 A:YVD401 2.7 24.7 0.6
H391 A:YVD401 2.7 25.3 0.4
HE21 A:GLN192 3.1 27.5 1.0
HD23 A:LEU167 3.1 25.2 1.0
NE2 A:GLN192 3.1 22.9 1.0
HD22 A:LEU167 3.1 25.2 1.0
HD21 A:LEU167 3.2 25.2 1.0
CD A:GLN192 3.3 19.7 1.0
CD2 A:LEU167 3.3 21.0 1.0
HG3 A:GLN192 3.4 24.9 1.0
CB A:GLN192 3.4 17.9 1.0
CE A:MET165 3.4 26.3 1.0
HE1 A:MET165 3.4 31.6 1.0
HE22 A:GLN192 3.4 27.5 1.0
CG A:GLN192 3.5 20.7 1.0
C36 A:YVD401 3.8 20.0 0.4
C36 A:YVD401 3.8 20.2 0.6
C38 A:YVD401 3.8 19.7 0.6
C38 A:YVD401 3.8 19.9 0.4
H A:GLN192 3.9 21.3 1.0
OE1 A:GLN192 3.9 20.9 1.0
HB3 A:GLN192 3.9 21.6 1.0
SD A:MET165 4.1 25.9 1.0
HG3 A:MET165 4.2 26.0 1.0
HE2 A:MET165 4.2 31.6 1.0
O A:THR190 4.2 20.0 1.0
C37 A:YVD401 4.4 19.5 0.4
C37 A:YVD401 4.4 19.4 0.6
HD1 A:PHE185 4.4 25.0 1.0
N A:GLN192 4.4 17.7 1.0
CA A:GLN192 4.4 25.2 1.0
HA A:LEU167 4.5 20.9 1.0
HG2 A:GLN192 4.5 24.9 1.0
O A:HOH596 4.5 23.4 1.0
H361 A:YVD401 4.6 24.1 0.4
H361 A:YVD401 4.6 24.3 0.6
H381 A:YVD401 4.6 23.6 0.6
H381 A:YVD401 4.6 23.9 0.4
O A:GLN192 4.6 25.7 1.0
CG A:MET165 4.7 21.7 1.0
HB2 A:MET165 4.7 17.1 1.0
CG A:LEU167 4.8 19.3 1.0
C A:GLN192 4.9 21.5 1.0
HB3 A:PHE185 5.0 22.2 1.0
HA A:GLN189 5.0 28.1 1.0
HD3 A:PRO168 5.0 21.6 1.0

Fluorine binding site 4 out of 6 in 7maz

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Fluorine binding site 4 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:25.9
occ:0.39
 F40 A:YVD401 0.0 25.9 0.4
F40 A:YVD401 0.0 28.3 0.6
C34 A:YVD401 1.3 21.9 0.4
C34 A:YVD401 1.4 22.1 0.6
C35 A:YVD401 2.5 21.5 0.4
C39 A:YVD401 2.5 20.5 0.6
C39 A:YVD401 2.5 21.1 0.4
C35 A:YVD401 2.5 21.6 0.6
HB2 A:GLN192 2.6 21.6 1.0
HE3 A:MET165 2.7 31.6 1.0
H351 A:YVD401 2.7 25.8 0.4
H391 A:YVD401 2.7 24.7 0.6
H351 A:YVD401 2.7 25.9 0.6
H391 A:YVD401 2.7 25.3 0.4
HE21 A:GLN192 3.1 27.5 1.0
NE2 A:GLN192 3.1 22.9 1.0
HD23 A:LEU167 3.1 25.2 1.0
HD22 A:LEU167 3.2 25.2 1.0
HD21 A:LEU167 3.2 25.2 1.0
CD A:GLN192 3.3 19.7 1.0
CD2 A:LEU167 3.3 21.0 1.0
HG3 A:GLN192 3.4 24.9 1.0
CE A:MET165 3.4 26.3 1.0
HE1 A:MET165 3.4 31.6 1.0
HE22 A:GLN192 3.4 27.5 1.0
CB A:GLN192 3.4 17.9 1.0
CG A:GLN192 3.5 20.7 1.0
C36 A:YVD401 3.8 20.0 0.4
C38 A:YVD401 3.8 19.7 0.6
C38 A:YVD401 3.8 19.9 0.4
C36 A:YVD401 3.9 20.2 0.6
OE1 A:GLN192 3.9 20.9 1.0
H A:GLN192 3.9 21.3 1.0
HB3 A:GLN192 3.9 21.6 1.0
SD A:MET165 4.1 25.9 1.0
HG3 A:MET165 4.2 26.0 1.0
HE2 A:MET165 4.2 31.6 1.0
O A:THR190 4.2 20.0 1.0
C37 A:YVD401 4.4 19.5 0.4
HD1 A:PHE185 4.4 25.0 1.0
C37 A:YVD401 4.4 19.4 0.6
CA A:GLN192 4.4 25.2 1.0
N A:GLN192 4.4 17.7 1.0
HG2 A:GLN192 4.5 24.9 1.0
HA A:LEU167 4.5 20.9 1.0
O A:HOH596 4.5 23.4 1.0
H361 A:YVD401 4.6 24.1 0.4
H381 A:YVD401 4.6 23.6 0.6
H381 A:YVD401 4.6 23.9 0.4
H361 A:YVD401 4.6 24.3 0.6
O A:GLN192 4.6 25.7 1.0
CG A:MET165 4.7 21.7 1.0
HB2 A:MET165 4.7 17.1 1.0
CG A:LEU167 4.8 19.3 1.0
C A:GLN192 4.9 21.5 1.0
HB3 A:PHE185 4.9 22.2 1.0
HA A:GLN189 5.0 28.1 1.0

Fluorine binding site 5 out of 6 in 7maz

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Fluorine binding site 5 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:46.6
occ:1.00
 F30 B:YVD401 0.0 46.6 1.0
C24 B:YVD401 1.4 41.2 1.0
N B:ARG188 2.4 34.4 1.0
C25 B:YVD401 2.5 39.1 1.0
C29 B:YVD401 2.5 35.7 1.0
HA B:ASP187 2.6 28.7 1.0
H B:ARG188 2.6 41.3 1.0
C B:ASP187 2.7 30.2 1.0
H291 B:YVD401 2.7 42.9 1.0
H251 B:YVD401 2.7 46.9 1.0
C B:ARG188 2.8 38.8 1.0
HA B:ARG188 2.8 42.9 1.0
CA B:ARG188 2.9 35.7 1.0
O B:ARG188 3.0 32.9 1.0
CA B:ASP187 3.1 23.9 1.0
O B:ASP187 3.2 28.3 1.0
HE3 B:MET49 3.3 59.1 1.0
H391 B:YVD401 3.3 32.9 1.0
N B:GLN189 3.4 35.7 1.0
HA B:GLN189 3.6 45.4 1.0
HB2 B:ASP187 3.7 32.8 1.0
H B:GLN189 3.8 42.9 1.0
O B:VAL186 3.8 24.4 1.0
C26 B:YVD401 3.8 33.2 1.0
C28 B:YVD401 3.9 32.4 1.0
HE2 B:MET49 3.9 59.1 1.0
CE B:MET49 3.9 49.3 1.0
CB B:ASP187 4.0 27.3 1.0
CA B:GLN189 4.0 37.9 1.0
HE1 B:MET49 4.1 59.1 1.0
C39 B:YVD401 4.1 27.4 1.0
H381 B:YVD401 4.1 36.3 1.0
HB2 B:GLN189 4.1 36.5 1.0
N B:ASP187 4.2 19.8 1.0
HE22 B:GLN192 4.3 37.7 1.0
C27 B:YVD401 4.3 22.5 1.0
SD B:MET165 4.4 30.1 1.0
CB B:ARG188 4.4 38.7 1.0
C B:VAL186 4.4 23.0 1.0
HB3 B:ASP187 4.4 32.8 1.0
HH B:TYR54 4.5 32.6 1.0
C38 B:YVD401 4.5 30.2 1.0
H261 B:YVD401 4.6 39.8 1.0
H281 B:YVD401 4.6 38.9 1.0
CB B:GLN189 4.6 30.4 1.0
HB3 B:ARG188 4.7 46.5 1.0
HE21 B:GLN192 4.8 37.7 1.0
HE2 B:MET165 4.8 29.4 1.0
H B:THR190 4.8 43.8 1.0
NE2 B:GLN192 4.9 31.4 1.0
HG2 B:ARG188 4.9 51.5 1.0
HB2 B:ARG188 4.9 46.5 1.0
H B:ASP187 4.9 23.8 1.0

Fluorine binding site 6 out of 6 in 7maz

Go back to Fluorine Binding Sites List in 7maz
Fluorine binding site 6 out of 6 in the Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:34.6
occ:1.00
 F40 B:YVD401 0.0 34.6 1.0
C34 B:YVD401 1.3 31.4 1.0
C39 B:YVD401 2.5 27.4 1.0
C35 B:YVD401 2.5 26.0 1.0
HE21 B:GLN192 2.6 37.7 1.0
H391 B:YVD401 2.7 32.9 1.0
H351 B:YVD401 2.7 31.2 1.0
NE2 B:GLN192 2.9 31.4 1.0
HB2 B:GLN192 2.9 38.0 1.0
HE3 B:MET165 3.0 29.4 1.0
HD23 B:LEU167 3.1 38.9 1.0
HE22 B:GLN192 3.1 37.7 1.0
HD22 B:LEU167 3.2 38.9 1.0
HD21 B:LEU167 3.4 38.9 1.0
CD2 B:LEU167 3.4 32.4 1.0
CD B:GLN192 3.5 29.0 1.0
HG3 B:GLN192 3.6 40.5 1.0
CB B:GLN192 3.8 31.6 1.0
C38 B:YVD401 3.8 30.2 1.0
CG B:GLN192 3.9 33.7 1.0
C36 B:YVD401 3.9 29.8 1.0
CE B:MET165 3.9 24.5 1.0
O B:THR190 4.0 34.1 1.0
HE2 B:MET165 4.1 29.4 1.0
HG3 B:MET165 4.1 24.1 1.0
H B:GLN192 4.1 38.7 1.0
OE1 B:GLN192 4.3 27.2 1.0
C37 B:YVD401 4.4 23.7 1.0
HB3 B:GLN192 4.4 38.0 1.0
HA B:LEU167 4.4 27.8 1.0
SD B:MET165 4.5 30.1 1.0
N B:GLN192 4.6 32.3 1.0
H381 B:YVD401 4.6 36.3 1.0
HE1 B:MET165 4.6 29.4 1.0
H361 B:YVD401 4.6 35.8 1.0
CA B:GLN192 4.7 27.6 1.0
CG B:MET165 4.7 20.0 1.0
O B:GLN192 4.7 36.8 1.0
HA B:GLN189 4.8 45.4 1.0
O B:ARG188 4.8 32.9 1.0
HB2 B:MET165 4.8 24.4 1.0
HG2 B:GLN192 4.8 40.5 1.0
HD3 B:PRO168 4.8 37.1 1.0
HD1 B:PHE185 4.9 33.4 1.0
CG B:LEU167 4.9 23.2 1.0
H B:THR190 4.9 43.8 1.0

Reference:

G.J.Lockbaum, C.A.Schiffer. Sars-Cov-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139 To Be Published.
Page generated: Fri Aug 2 09:24:22 2024

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