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Fluorine in PDB 9arq: Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) in Complex with An Inhibitor Tkb-245

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) in Complex with An Inhibitor Tkb-245

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) 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 (Authentic Protein) in Complex with An Inhibitor Tkb-245, PDB code: 9arq was solved by H.Bulut, S.Hattori, H.Hayashi, K.Hasegawa, M.Li, A.Wlodawer, H.Tamamura, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.92 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.627, 63.997, 105.646, 90, 90, 90
R / Rfree (%) 18.1 / 23.6

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 4 in 9arq

Go back to Fluorine Binding Sites List in 9arq
Fluorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) 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 (Authentic Protein) in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:43.2
occ:1.00
 FBS A:T2L401 0.0 43.2 1.0
CBN A:T2L401 1.2 43.9 1.0
CBO A:T2L401 2.2 45.5 1.0
CBK A:T2L401 2.2 39.4 1.0
NBJ A:T2L401 2.9 35.5 1.0
ND1 A:HIS41 3.2 34.0 1.0
SD A:MET49 3.3 65.9 1.0
CBP A:T2L401 3.4 53.1 1.0
CBL A:T2L401 3.4 49.6 1.0
CAQ A:T2L401 3.6 23.1 1.0
CE1 A:HIS41 3.6 33.2 1.0
CBQ A:T2L401 3.9 55.5 1.0
CAP A:T2L401 4.0 24.0 1.0
CE A:MET49 4.0 64.5 1.0
CBI A:T2L401 4.2 34.9 1.0
CBH A:T2L401 4.2 28.5 1.0
CG A:MET49 4.2 52.4 1.0
CG A:HIS41 4.3 26.4 1.0
O A:HIS41 4.4 21.8 1.0
CBF A:T2L401 4.4 26.9 1.0
OAK A:T2L401 4.5 21.2 1.0
CAJ A:T2L401 4.6 23.5 1.0
NE2 A:HIS41 4.7 35.0 1.0
SBM A:T2L401 4.7 41.9 1.0
CAM A:T2L401 4.7 24.6 1.0
CB A:HIS41 4.7 25.2 1.0

Fluorine binding site 2 out of 4 in 9arq

Go back to Fluorine Binding Sites List in 9arq
Fluorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) 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 (Authentic Protein) in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.6
occ:1.00
 FAX A:T2L401 0.0 41.6 1.0
CAV A:T2L401 1.2 36.0 1.0
FAY A:T2L401 1.9 40.6 1.0
FAW A:T2L401 2.1 39.7 1.0
CAU A:T2L401 2.3 31.3 1.0
NAT A:T2L401 3.0 24.4 1.0
O A:HOH541 3.0 34.8 1.0
OAZ A:T2L401 3.2 31.5 1.0
O A:GLU166 3.3 21.2 1.0
CA A:LEU167 3.8 27.1 1.0
CD A:PRO168 3.9 30.0 1.0
CD2 A:LEU167 4.0 27.6 1.0
O A:THR190 4.2 37.9 1.0
C A:GLU166 4.2 23.4 1.0
O A:GLN192 4.3 31.9 1.0
CAS A:T2L401 4.4 22.8 1.0
CE A:MET165 4.4 53.0 1.0
N A:LEU167 4.4 25.6 1.0
CB A:LEU167 4.5 28.6 1.0
C A:LEU167 4.5 32.5 1.0
N A:PRO168 4.6 33.0 1.0
CG A:LEU167 4.6 28.4 1.0
CBB A:T2L401 4.7 24.9 1.0
CG A:PRO168 4.8 31.9 1.0
CB A:GLN192 4.8 30.4 1.0
N A:GLN192 5.0 37.3 1.0
CBA A:T2L401 5.0 23.1 1.0

Fluorine binding site 3 out of 4 in 9arq

Go back to Fluorine Binding Sites List in 9arq
Fluorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) 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 (Authentic Protein) in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:40.6
occ:1.00
 FAY A:T2L401 0.0 40.6 1.0
CAV A:T2L401 1.3 36.0 1.0
FAX A:T2L401 1.9 41.6 1.0
FAW A:T2L401 2.0 39.7 1.0
CAU A:T2L401 2.3 31.3 1.0
NAT A:T2L401 2.7 24.4 1.0
CE A:MET165 2.8 53.0 1.0
O A:GLU166 3.0 21.2 1.0
CD2 A:LEU167 3.4 27.6 1.0
OAZ A:T2L401 3.4 31.5 1.0
C A:GLU166 3.7 23.4 1.0
CA A:LEU167 3.9 27.1 1.0
SD A:MET165 3.9 40.6 1.0
CG A:MET165 3.9 36.5 1.0
CG A:LEU167 3.9 28.4 1.0
N A:LEU167 4.1 25.6 1.0
CB A:MET165 4.1 28.3 1.0
CAS A:T2L401 4.1 22.8 1.0
O A:HOH541 4.2 34.8 1.0
CB A:LEU167 4.4 28.6 1.0
NE2 A:GLN192 4.5 30.3 1.0
N A:GLU166 4.5 21.8 1.0
CAR A:T2L401 4.6 23.0 1.0
OBE A:T2L401 4.7 22.4 1.0
CA A:GLU166 4.7 22.4 1.0
CD A:GLN192 4.9 29.2 1.0
CB A:GLN192 5.0 30.4 1.0

Fluorine binding site 4 out of 4 in 9arq

Go back to Fluorine Binding Sites List in 9arq
Fluorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Main Protease (Authentic Protein) 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 (Authentic Protein) in Complex with An Inhibitor Tkb-245 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.7
occ:1.00
 FAW A:T2L401 0.0 39.7 1.0
CAV A:T2L401 1.2 36.0 1.0
FAY A:T2L401 2.0 40.6 1.0
FAX A:T2L401 2.1 41.6 1.0
CAU A:T2L401 2.3 31.3 1.0
OAZ A:T2L401 2.6 31.5 1.0
O A:THR190 3.0 37.9 1.0
CE A:MET165 3.0 53.0 1.0
NE2 A:GLN192 3.2 30.3 1.0
NAT A:T2L401 3.4 24.4 1.0
CD A:GLN192 3.8 29.2 1.0
O A:ARG188 3.9 25.8 1.0
CG A:GLN192 4.0 28.1 1.0
CB A:GLN192 4.0 30.4 1.0
N A:THR190 4.2 35.4 1.0
C A:THR190 4.2 36.8 1.0
CD2 A:LEU167 4.3 27.6 1.0
N A:GLN192 4.6 37.3 1.0
OE1 A:GLN192 4.6 30.1 1.0
CAS A:T2L401 4.7 22.8 1.0
O A:GLU166 4.7 21.2 1.0
SD A:MET165 4.7 40.6 1.0
CA A:GLN189 4.8 28.9 1.0
O A:GLN192 4.9 31.9 1.0
CA A:GLN192 4.9 33.3 1.0
CA A:THR190 4.9 36.6 1.0
C A:ARG188 5.0 25.6 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.
Page generated: Wed Jul 16 10:20:03 2025

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