Fluorine in PDB 9ars: Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245, PDB code: 9ars was solved by H.Bulut, S.Hattori, H.Hayashi, K.Hasegawa, M.Li, A.Wlodawer, S.Misumi, H.Tamamura, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.931, 53.951, 114.966, 90, 100.38, 90
R / Rfree (%) 17.8 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 (pdb code 9ars). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245, PDB code: 9ars:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 9ars

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Fluorine binding site 1 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:58.1
occ:1.00
 FBS A:T2L401 0.0 58.1 1.0
CBN A:T2L401 1.5 72.1 1.0
CBO A:T2L401 2.5 67.3 1.0
CBK A:T2L401 2.5 68.7 1.0
NBJ A:T2L401 3.1 53.8 1.0
CBP A:T2L401 3.7 64.3 1.0
CBL A:T2L401 3.8 65.1 1.0
CBQ A:T2L401 4.2 62.9 1.0
CBI A:T2L401 4.4 52.1 1.0
CG2 A:THR25 4.7 64.9 1.0
CE A:MET49 4.7 77.7 1.0
SBM A:T2L401 5.0 51.1 1.0

Fluorine binding site 2 out of 8 in 9ars

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Fluorine binding site 2 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:75.8
occ:1.00
 FAX A:T2L401 0.0 75.8 1.0
CAV A:T2L401 1.4 65.5 1.0
FAW A:T2L401 2.1 59.4 1.0
FAY A:T2L401 2.3 78.6 1.0
O A:THR190 2.4 47.6 1.0
CAU A:T2L401 2.4 54.8 1.0
OAZ A:T2L401 2.8 51.3 1.0
C A:THR190 3.5 46.1 1.0
NE2 A:GLN192 3.6 42.9 1.0
NAT A:T2L401 3.6 48.9 1.0
N A:GLN192 3.7 46.1 1.0
CE A:MET165 3.8 62.3 1.0
CG A:GLN192 3.9 40.7 1.0
CB A:GLN192 3.9 37.4 1.0
CD A:GLN192 4.1 41.3 1.0
N A:THR190 4.2 50.6 1.0
CA A:ALA191 4.2 58.0 1.0
C A:ALA191 4.3 53.1 1.0
N A:ALA191 4.3 55.2 1.0
CA A:GLN192 4.4 41.6 1.0
CD2 A:LEU167 4.4 48.9 1.0
O A:ARG188 4.5 36.7 1.0
CA A:THR190 4.5 48.6 1.0
O A:GLN192 4.7 55.1 1.0
CD A:PRO168 4.7 62.5 1.0
CAS A:T2L401 4.8 49.5 1.0
O A:VAL166 5.0 44.0 1.0

Fluorine binding site 3 out of 8 in 9ars

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Fluorine binding site 3 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:78.6
occ:1.00
 FAY A:T2L401 0.0 78.6 1.0
CAV A:T2L401 1.4 65.5 1.0
FAW A:T2L401 2.2 59.4 1.0
FAX A:T2L401 2.3 75.8 1.0
CAU A:T2L401 2.4 54.8 1.0
NAT A:T2L401 2.9 48.9 1.0
OAZ A:T2L401 3.3 51.3 1.0
CD A:PRO168 3.5 62.5 1.0
O A:VAL166 3.9 44.0 1.0
O A:THR190 4.0 47.6 1.0
CBB A:T2L401 4.1 48.3 1.0
CG A:PRO168 4.1 63.9 1.0
N A:PRO168 4.2 54.3 1.0
CAS A:T2L401 4.3 49.5 1.0
CA A:LEU167 4.4 48.0 1.0
C A:LEU167 4.6 53.1 1.0
N A:GLN192 4.7 46.1 1.0
CBA A:T2L401 4.8 49.4 1.0
C A:THR190 4.9 46.1 1.0
CD2 A:LEU167 4.9 48.9 1.0
C A:VAL166 4.9 44.8 1.0
CA A:ALA191 4.9 58.0 1.0

Fluorine binding site 4 out of 8 in 9ars

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Fluorine binding site 4 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:59.4
occ:1.00
 FAW A:T2L401 0.0 59.4 1.0
CAV A:T2L401 1.3 65.5 1.0
FAX A:T2L401 2.1 75.8 1.0
FAY A:T2L401 2.2 78.6 1.0
CAU A:T2L401 2.3 54.8 1.0
NAT A:T2L401 2.7 48.9 1.0
O A:VAL166 3.0 44.0 1.0
CE A:MET165 3.1 62.3 1.0
CD2 A:LEU167 3.2 48.9 1.0
OAZ A:T2L401 3.3 51.3 1.0
CA A:LEU167 3.7 48.0 1.0
C A:VAL166 3.8 44.8 1.0
CD A:PRO168 4.1 62.5 1.0
CG A:LEU167 4.1 49.1 1.0
CAS A:T2L401 4.1 49.5 1.0
N A:LEU167 4.2 44.6 1.0
CB A:LEU167 4.3 45.8 1.0
O A:THR190 4.5 47.6 1.0
NE2 A:GLN192 4.6 42.9 1.0
C A:LEU167 4.6 53.1 1.0
CAR A:T2L401 4.7 43.1 1.0
SD A:MET165 4.7 59.7 1.0
N A:PRO168 4.7 54.3 1.0
OBE A:T2L401 4.8 45.2 1.0
CG A:MET165 4.9 53.1 1.0
CB A:GLN192 4.9 37.4 1.0

Fluorine binding site 5 out of 8 in 9ars

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Fluorine binding site 5 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:50.2
occ:1.00
 FBS B:T2L401 0.0 50.2 1.0
CBN B:T2L401 1.4 54.6 1.0
CBO B:T2L401 2.4 52.6 1.0
CBK B:T2L401 2.4 54.2 1.0
NBJ B:T2L401 3.0 46.0 1.0
CBP B:T2L401 3.6 55.0 1.0
CBL B:T2L401 3.7 55.6 1.0
CBQ B:T2L401 4.1 55.4 1.0
CBI B:T2L401 4.3 45.4 1.0
OG B:SER46 4.4 94.0 1.0
CE B:MET49 4.8 73.6 1.0
SBM B:T2L401 5.0 44.5 1.0

Fluorine binding site 6 out of 8 in 9ars

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Fluorine binding site 6 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:59.0
occ:1.00
 FAX B:T2L401 0.0 59.0 1.0
CAV B:T2L401 1.4 57.9 1.0
FAW B:T2L401 2.2 63.6 1.0
FAY B:T2L401 2.3 53.3 1.0
CAU B:T2L401 2.5 52.7 1.0
O B:THR190 2.7 53.0 1.0
OAZ B:T2L401 2.8 47.7 1.0
CG B:GLN192 3.2 48.9 1.0
NAT B:T2L401 3.7 47.8 1.0
NE2 B:GLN192 3.7 43.8 1.0
C B:THR190 3.9 54.1 1.0
CD B:GLN192 3.9 47.5 1.0
N B:GLN192 4.0 54.2 1.0
O B:GLN192 4.1 51.6 1.0
CD2 B:LEU167 4.2 48.5 1.0
N B:THR190 4.2 50.3 1.0
CB B:GLN192 4.4 44.6 1.0
CE B:MET165 4.6 60.7 1.0
CA B:GLN192 4.6 49.5 1.0
O B:ARG188 4.6 45.2 1.0
C B:ALA191 4.7 59.7 1.0
C B:GLN192 4.7 54.0 1.0
CA B:THR190 4.8 54.9 1.0
N B:ALA191 4.8 63.9 1.0
CD B:PRO168 4.9 79.0 1.0
CA B:ALA191 4.9 64.5 1.0
O B:VAL166 4.9 38.2 1.0
CAS B:T2L401 4.9 47.9 1.0

Fluorine binding site 7 out of 8 in 9ars

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Fluorine binding site 7 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:53.3
occ:1.00
 FAY B:T2L401 0.0 53.3 1.0
CAV B:T2L401 1.4 57.9 1.0
FAW B:T2L401 2.2 63.6 1.0
FAX B:T2L401 2.3 59.0 1.0
CAU B:T2L401 2.5 52.7 1.0
NAT B:T2L401 2.9 47.8 1.0
O B:VAL166 3.1 38.2 1.0
CD B:PRO168 3.4 79.0 1.0
CA B:LEU167 3.4 49.8 1.0
OAZ B:T2L401 3.5 47.7 1.0
N B:PRO168 3.8 75.4 1.0
CD2 B:LEU167 3.9 48.5 1.0
CG B:PRO168 3.9 80.1 1.0
C B:LEU167 3.9 60.3 1.0
C B:VAL166 4.0 37.1 1.0
N B:LEU167 4.2 40.8 1.0
O B:GLN192 4.3 51.6 1.0
CAS B:T2L401 4.3 47.9 1.0
CB B:LEU167 4.4 48.2 1.0
CBD B:T2L401 4.5 52.7 1.0
CG B:LEU167 4.6 49.9 1.0
O B:THR190 4.7 53.0 1.0
CA B:PRO168 4.7 79.0 1.0
CBA B:T2L401 4.9 50.3 1.0
O B:LEU167 5.0 59.0 1.0
CG B:GLN192 5.0 48.9 1.0

Fluorine binding site 8 out of 8 in 9ars

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Fluorine binding site 8 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Sars-Cov-2 Main Protease E166V Mutant in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:63.6
occ:1.00
 FAW B:T2L401 0.0 63.6 1.0
CAV B:T2L401 1.3 57.9 1.0
FAX B:T2L401 2.2 59.0 1.0
FAY B:T2L401 2.2 53.3 1.0
CAU B:T2L401 2.3 52.7 1.0
NAT B:T2L401 2.8 47.8 1.0
OAZ B:T2L401 3.1 47.7 1.0
CE B:MET165 3.2 60.7 1.0
O B:VAL166 3.2 38.2 1.0
CD2 B:LEU167 3.3 48.5 1.0
SD B:MET165 3.8 56.5 1.0
CG B:MET165 3.9 52.8 1.0
C B:VAL166 4.0 37.1 1.0
CA B:LEU167 4.1 49.8 1.0
CAS B:T2L401 4.1 47.9 1.0
CG B:LEU167 4.2 49.9 1.0
NE2 B:GLN192 4.2 43.8 1.0
CG B:GLN192 4.2 48.9 1.0
N B:LEU167 4.4 40.8 1.0
CB B:MET165 4.4 45.8 1.0
CD B:GLN192 4.5 47.5 1.0
CAR B:T2L401 4.5 38.8 1.0
OBE B:T2L401 4.6 39.9 1.0
CB B:LEU167 4.6 48.2 1.0
O B:THR190 4.8 53.0 1.0
N B:VAL166 4.8 34.6 1.0

Reference:

S.Hattori, H.Bulut, H.Hayashi, N.Kishimoto, N.Takamune, K.Hasegawa, K.Murayama, L.Mi, A.Wlodawer, H.Tamamura, S.Misumi, H.Mitsuya. Structural and Virologic Mechanism of Emergence of Main Protease Inhibitor-Resistance in Sars-Cov-2 As Selected with Main Protease Inhibitors To Be Published.
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