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Fluorine in PDB 8d4p: Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1

Enzymatic activity of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1, PDB code: 8d4p was solved by S.G.Butler, Y.Chen, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.42 / 2.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.643, 53.607, 45.029, 90, 101.86, 90
R / Rfree (%) 18.9 / 25.7

Other elements in 8d4p:

The structure of Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 (pdb code 8d4p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1, PDB code: 8d4p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8d4p

Go back to Fluorine Binding Sites List in 8d4p
Fluorine binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:94.1
occ:1.00
 F17 A:QAO401 0.0 94.1 1.0
C16 A:QAO401 1.4 95.6 1.0
C18 A:QAO401 2.4 95.3 1.0
C15 A:QAO401 2.4 96.8 1.0
O A:THR190 3.1 49.0 1.0
CE A:MET165 3.2 56.2 1.0
O A:ARG188 3.3 37.6 1.0
NE2 A:GLN192 3.5 40.2 1.0
C12 A:QAO401 3.7 89.9 1.0
C14 A:QAO401 3.7 92.5 1.0
N A:THR190 3.9 46.1 1.0
CA A:GLN189 4.1 47.9 1.0
C A:THR190 4.1 51.2 1.0
C13 A:QAO401 4.2 94.6 1.0
O A:GLU166 4.2 39.5 1.0
C A:ARG188 4.3 41.2 1.0
CD2 A:LEU167 4.4 54.7 1.0
SD A:MET165 4.4 61.4 1.0
C A:GLN189 4.5 46.1 1.0
CD A:GLN192 4.5 42.6 1.0
N A:GLN189 4.6 40.8 1.0
CD A:PRO168 4.7 54.9 1.0
CA A:THR190 4.7 51.9 1.0
CG A:GLN192 4.7 46.1 1.0
CA A:LEU167 4.9 45.7 1.0
C11 A:QAO401 4.9 77.8 1.0

Fluorine binding site 2 out of 6 in 8d4p

Go back to Fluorine Binding Sites List in 8d4p
Fluorine binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:105.3
occ:1.00
 F33 A:QAO401 0.0 105.3 1.0
S32 A:QAO401 1.6 104.2 1.0
F36 A:QAO401 1.8 106.9 1.0
F37 A:QAO401 2.4 114.7 1.0
C31 A:QAO401 2.5 85.5 1.0
C30 A:QAO401 2.8 69.7 1.0
F34 A:QAO401 3.0 107.0 1.0
F35 A:QAO401 3.0 116.8 1.0
CB A:HIS41 3.2 39.0 1.0
CG A:MET49 3.5 73.5 1.0
CG A:HIS41 3.5 41.9 1.0
C28 A:QAO401 3.7 71.7 1.0
CD2 A:HIS41 3.7 46.3 1.0
CB A:CYS44 4.1 44.9 1.0
CB A:MET49 4.1 72.2 1.0
O A:HIS41 4.1 35.3 1.0
SD A:MET49 4.1 82.0 1.0
C29 A:QAO401 4.2 61.4 1.0
CA A:HIS41 4.3 38.1 1.0
OH A:TYR54 4.3 34.5 1.0
SG A:CYS44 4.4 50.2 1.0
ND1 A:HIS41 4.4 43.0 1.0
C A:HIS41 4.6 35.3 1.0
NE2 A:HIS41 4.7 47.9 1.0
CA A:MET49 4.7 65.6 1.0
C27 A:QAO401 4.8 64.7 1.0
C26 A:QAO401 4.9 58.1 1.0

Fluorine binding site 3 out of 6 in 8d4p

Go back to Fluorine Binding Sites List in 8d4p
Fluorine binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:107.0
occ:1.00
 F34 A:QAO401 0.0 107.0 1.0
S32 A:QAO401 1.6 104.2 1.0
C31 A:QAO401 2.0 85.5 1.0
F35 A:QAO401 2.3 116.8 1.0
F36 A:QAO401 2.3 106.9 1.0
C30 A:QAO401 2.8 69.7 1.0
C28 A:QAO401 2.8 71.7 1.0
F37 A:QAO401 2.9 114.7 1.0
F33 A:QAO401 3.0 105.3 1.0
N A:GLN189 3.9 40.8 1.0
C29 A:QAO401 3.9 61.4 1.0
C27 A:QAO401 3.9 64.7 1.0
C10 A:QAO401 4.0 69.7 1.0
CB A:GLN189 4.0 48.4 1.0
CB A:MET49 4.1 72.2 1.0
C A:ARG188 4.2 41.2 1.0
CA A:GLN189 4.3 47.9 1.0
O A:MET49 4.4 51.2 1.0
C26 A:QAO401 4.4 58.1 1.0
CG A:MET49 4.4 73.5 1.0
N09 A:QAO401 4.5 66.1 1.0
CA A:ARG188 4.5 41.7 1.0
SD A:MET49 4.7 82.0 1.0
O A:ARG188 4.9 37.6 1.0
N A:ARG188 4.9 42.0 1.0
CE A:MET165 4.9 56.2 1.0
CA A:MET49 4.9 65.6 1.0
OE1 A:GLN189 5.0 56.7 1.0

Fluorine binding site 4 out of 6 in 8d4p

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Fluorine binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:116.8
occ:1.00
 F35 A:QAO401 0.0 116.8 1.0
S32 A:QAO401 1.6 104.2 1.0
F37 A:QAO401 1.8 114.7 1.0
F34 A:QAO401 2.3 107.0 1.0
F36 A:QAO401 2.3 106.9 1.0
F33 A:QAO401 3.0 105.3 1.0
O A:ASP187 3.1 35.6 1.0
CA A:ARG188 3.1 41.7 1.0
C31 A:QAO401 3.1 85.5 1.0
C A:ASP187 3.1 36.9 1.0
N A:ARG188 3.2 42.0 1.0
C28 A:QAO401 3.6 71.7 1.0
C A:ARG188 3.6 41.2 1.0
OH A:TYR54 3.9 34.5 1.0
N A:GLN189 3.9 40.8 1.0
CA A:ASP187 4.0 34.1 1.0
O A:MET49 4.2 51.2 1.0
C30 A:QAO401 4.3 69.7 1.0
CB A:ASP187 4.4 33.1 1.0
O A:ARG188 4.4 37.6 1.0
CB A:ARG188 4.4 46.4 1.0
CB A:HIS41 4.5 39.0 1.0
CE A:MET165 4.7 56.2 1.0
CG A:HIS41 4.8 41.9 1.0
CB A:MET49 4.9 72.2 1.0
C27 A:QAO401 4.9 64.7 1.0
CA A:GLN189 5.0 47.9 1.0

Fluorine binding site 5 out of 6 in 8d4p

Go back to Fluorine Binding Sites List in 8d4p
Fluorine binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:106.9
occ:1.00
 F36 A:QAO401 0.0 106.9 1.0
S32 A:QAO401 1.6 104.2 1.0
F33 A:QAO401 1.8 105.3 1.0
F34 A:QAO401 2.3 107.0 1.0
F35 A:QAO401 2.3 116.8 1.0
CB A:MET49 2.8 72.2 1.0
CG A:MET49 2.8 73.5 1.0
F37 A:QAO401 3.0 114.7 1.0
C31 A:QAO401 3.2 85.5 1.0
CA A:MET49 3.3 65.6 1.0
O A:MET49 3.5 51.2 1.0
C30 A:QAO401 3.7 69.7 1.0
C A:MET49 3.9 56.4 1.0
SD A:MET49 3.9 82.0 1.0
C28 A:QAO401 4.3 71.7 1.0
OH A:TYR54 4.4 34.5 1.0
N A:GLN189 4.6 40.8 1.0
CA A:ARG188 4.6 41.7 1.0
CB A:HIS41 4.6 39.0 1.0
N A:MET49 4.6 66.8 1.0
CB A:CYS44 4.6 44.9 1.0
SG A:CYS44 4.6 50.2 1.0
O A:ASP187 4.7 35.6 1.0
CE A:MET49 4.8 70.9 1.0
C A:ARG188 4.9 41.2 1.0

Fluorine binding site 6 out of 6 in 8d4p

Go back to Fluorine Binding Sites List in 8d4p
Fluorine binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1


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 the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:114.7
occ:1.00
 F37 A:QAO401 0.0 114.7 1.0
S32 A:QAO401 1.6 104.2 1.0
F35 A:QAO401 1.8 116.8 1.0
F33 A:QAO401 2.4 105.3 1.0
C31 A:QAO401 2.4 85.5 1.0
C28 A:QAO401 2.7 71.7 1.0
F34 A:QAO401 2.9 107.0 1.0
CB A:HIS41 2.9 39.0 1.0
F36 A:QAO401 3.0 106.9 1.0
CG A:HIS41 3.1 41.9 1.0
ND1 A:HIS41 3.3 43.0 1.0
C30 A:QAO401 3.7 69.7 1.0
OH A:TYR54 3.7 34.5 1.0
CD2 A:HIS41 3.8 46.3 1.0
O A:ASP187 3.9 35.6 1.0
C27 A:QAO401 4.0 64.7 1.0
C A:ASP187 4.0 36.9 1.0
CE1 A:HIS41 4.1 46.4 1.0
CB A:ASP187 4.1 33.1 1.0
CA A:ASP187 4.3 34.1 1.0
NE2 A:HIS41 4.3 47.9 1.0
CA A:HIS41 4.4 38.1 1.0
O A:HOH533 4.5 28.7 1.0
N A:ARG188 4.5 42.0 1.0
C29 A:QAO401 4.7 61.4 1.0
CA A:ARG188 4.8 41.7 1.0
C26 A:QAO401 4.8 58.1 1.0

Reference:

S.G.Butler, Y.Chen, J.Wang. Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor JUN10-90-3-C1 To Be Published.
Page generated: Wed Jul 16 03:19:50 2025

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