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Fluorine in PDB 7mng: Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy):
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy), PDB code: 7mng was solved by B.Andi, D.Kumaran, A.S.Soares, D.F.Kreitler, W.Shi, J.Jakoncic, M.R.Fuchs, J.Keereetaweep, J.Shanklin, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.16 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.706, 53.896, 44.75, 90, 101.1, 90
R / Rfree (%) 18 / 21.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) (pdb code 7mng). 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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy), PDB code: 7mng:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7mng

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Fluorine binding site 1 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.2
occ:0.35
 F1 A:ZL7401 0.0 38.2 0.3
C15 A:ZL7401 1.4 37.9 0.3
C14 A:ZL7401 2.3 38.2 0.3
C16 A:ZL7401 2.4 40.4 0.3
O A:HIS41 2.6 23.4 1.0
O A:CYS44 3.0 33.5 1.0
CB A:CYS44 3.4 26.3 1.0
C13 A:ZL7401 3.6 40.0 0.3
C A:CYS44 3.6 31.5 1.0
C17 A:ZL7401 3.6 43.4 0.3
CG2 A:THR25 3.7 32.4 1.0
C A:HIS41 3.8 21.0 1.0
CD2 A:HIS41 3.9 23.6 1.0
CA A:CYS44 3.9 27.1 1.0
SD A:MET49 3.9 42.7 1.0
N A:CYS44 4.1 26.7 1.0
C12 A:ZL7401 4.1 45.2 0.5
CG A:MET49 4.2 43.3 1.0
OG1 A:THR25 4.2 30.5 1.0
CB A:HIS41 4.3 20.6 1.0
CG A:HIS41 4.5 21.3 1.0
N A:THR45 4.5 33.5 1.0
CB A:THR25 4.5 30.6 1.0
CA A:HIS41 4.6 20.5 1.0
SG A:CYS44 4.7 30.3 1.0
C17 A:ZL7401 4.7 76.2 0.7
N A:VAL42 4.7 19.4 1.0
C22 A:ZL7401 4.8 60.4 0.5
C A:THR45 4.9 42.3 1.0
CA A:THR45 4.9 41.0 1.0
CA A:VAL42 4.9 19.8 1.0
C A:VAL42 4.9 22.4 1.0
C22 A:ZL7401 4.9 61.0 0.5
NE2 A:HIS41 5.0 23.7 1.0

Fluorine binding site 2 out of 8 in 7mng

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Fluorine binding site 2 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.0
occ:0.65
 F1 A:ZL7401 0.0 56.0 0.7
C15 A:ZL7401 1.4 70.0 0.7
O A:HOH759 1.9 30.0 0.5
C16 A:ZL7401 2.3 74.7 0.7
C14 A:ZL7401 2.3 63.9 0.7
O A:HOH501 2.5 30.0 0.5
CG A:MET165 3.3 29.0 0.5
O A:HIS164 3.6 20.2 1.0
C17 A:ZL7401 3.6 76.2 0.7
C13 A:ZL7401 3.6 75.3 0.7
O A:HOH672 3.6 49.0 1.0
CE A:MET49 3.6 40.8 1.0
C12 A:ZL7401 4.1 80.9 0.5
CG A:MET165 4.1 29.0 0.5
CB A:MET165 4.2 26.8 0.5
CB A:MET165 4.2 26.8 0.5
C1 A:ZL7401 4.2 50.3 0.5
CE1 A:HIS41 4.3 25.8 1.0
ND1 A:HIS41 4.3 26.1 1.0
CA A:MET165 4.3 23.0 0.5
O4 A:ZL7401 4.4 65.2 0.5
CA A:MET165 4.4 23.0 0.5
O4 A:ZL7401 4.4 58.1 0.5
C1 A:ZL7401 4.4 57.8 0.5
SD A:MET165 4.4 38.8 0.5
SD A:MET165 4.4 38.8 0.5
CE A:MET165 4.4 37.2 0.5
C A:HIS164 4.5 18.8 1.0
O A:HOH702 4.7 54.9 1.0
CA A:ASP187 4.7 20.0 1.0
N A:ARG188 4.7 23.0 1.0
C A:ASP187 4.7 22.1 1.0
NE2 A:HIS41 4.8 23.7 1.0
CG A:HIS41 4.8 21.3 1.0
F2 A:ZL7401 4.8 54.9 0.5
CB A:ASP187 4.9 19.0 1.0
C13 A:ZL7401 4.9 40.0 0.3
N A:MET165 4.9 18.3 1.0

Fluorine binding site 3 out of 8 in 7mng

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Fluorine binding site 3 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.9
occ:0.50
 F2 A:ZL7401 0.0 54.9 0.5
F2 A:ZL7401 1.2 85.7 0.5
C18 A:ZL7401 1.3 57.2 0.3
C12 A:ZL7401 1.6 80.9 0.5
C13 A:ZL7401 1.6 75.3 0.7
C18 A:ZL7401 1.7 86.3 0.7
C11 A:ZL7401 1.9 81.2 0.5
F3 A:ZL7401 2.1 76.7 0.5
F4 A:ZL7401 2.1 54.7 0.5
C11 A:ZL7401 2.4 48.8 0.5
F3 A:ZL7401 2.5 85.9 0.5
C17 A:ZL7401 2.8 76.2 0.7
C14 A:ZL7401 2.8 63.9 0.7
C12 A:ZL7401 2.8 45.2 0.5
O A:HOH745 2.8 30.0 0.8
F4 A:ZL7401 2.9 85.3 0.5
C13 A:ZL7401 3.0 40.0 0.3
N2 A:ZL7401 3.1 78.6 0.5
N2 A:ZL7401 3.2 52.7 0.5
CG A:MET49 3.5 43.3 1.0
C15 A:ZL7401 3.5 70.0 0.7
C16 A:ZL7401 3.6 74.7 0.7
NE2 A:GLN189 3.6 44.5 0.8
CB A:MET49 3.7 41.4 1.0
C17 A:ZL7401 3.9 43.4 0.3
C14 A:ZL7401 4.2 38.2 0.3
C5 A:ZL7401 4.4 76.3 0.5
CB A:GLN189 4.4 32.8 1.0
CD A:GLN189 4.4 41.5 0.8
C5 A:ZL7401 4.5 53.0 0.5
CE A:MET49 4.5 40.8 1.0
F1 A:ZL7401 4.8 56.0 0.7
CG A:GLN189 4.8 38.0 1.0
SD A:MET49 4.8 42.7 1.0
C16 A:ZL7401 4.8 40.4 0.3
C15 A:ZL7401 4.9 37.9 0.3
O A:HOH662 4.9 52.4 1.0
O A:HOH757 4.9 49.2 1.0
O A:HOH501 4.9 30.0 0.5
N1 A:ZL7401 5.0 62.0 0.5

Fluorine binding site 4 out of 8 in 7mng

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Fluorine binding site 4 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:85.7
occ:0.50
 F2 A:ZL7401 0.0 85.7 0.5
C18 A:ZL7401 1.2 57.2 0.3
F2 A:ZL7401 1.2 54.9 0.5
F3 A:ZL7401 1.3 76.7 0.5
C18 A:ZL7401 1.3 86.3 0.7
F4 A:ZL7401 1.6 54.7 0.5
F4 A:ZL7401 2.2 85.3 0.5
F3 A:ZL7401 2.2 85.9 0.5
C11 A:ZL7401 2.4 81.2 0.5
O A:HOH745 2.4 30.0 0.8
C13 A:ZL7401 2.4 75.3 0.7
C12 A:ZL7401 2.6 80.9 0.5
C11 A:ZL7401 2.7 48.8 0.5
NE2 A:GLN189 2.7 44.5 0.8
N2 A:ZL7401 3.4 78.6 0.5
CD A:GLN189 3.5 41.5 0.8
C12 A:ZL7401 3.5 45.2 0.5
N2 A:ZL7401 3.5 52.7 0.5
C14 A:ZL7401 3.6 63.9 0.7
C17 A:ZL7401 3.9 76.2 0.7
CB A:MET49 4.0 41.4 1.0
C13 A:ZL7401 4.0 40.0 0.3
CB A:GLN189 4.1 32.8 1.0
CG A:GLN189 4.1 38.0 1.0
OE1 A:GLN189 4.1 44.8 0.8
CG A:MET49 4.2 43.3 1.0
C17 A:ZL7401 4.4 43.4 0.3
C15 A:ZL7401 4.6 70.0 0.7
O A:HOH756 4.7 36.3 1.0
O A:HOH662 4.7 52.4 1.0
C5 A:ZL7401 4.8 76.3 0.5
C16 A:ZL7401 4.8 74.7 0.7
O A:HOH757 4.9 49.2 1.0
C5 A:ZL7401 5.0 53.0 0.5

Fluorine binding site 5 out of 8 in 7mng

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Fluorine binding site 5 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:76.7
occ:0.50
 F3 A:ZL7401 0.0 76.7 0.5
F3 A:ZL7401 1.0 85.9 0.5
C18 A:ZL7401 1.0 86.3 0.7
C18 A:ZL7401 1.3 57.2 0.3
F2 A:ZL7401 1.3 85.7 0.5
F4 A:ZL7401 1.7 85.3 0.5
F2 A:ZL7401 2.1 54.9 0.5
F4 A:ZL7401 2.2 54.7 0.5
C11 A:ZL7401 2.4 48.8 0.5
C11 A:ZL7401 2.5 81.2 0.5
NE2 A:GLN189 2.9 44.5 0.8
C12 A:ZL7401 3.2 45.2 0.5
C12 A:ZL7401 3.3 80.9 0.5
N2 A:ZL7401 3.4 78.6 0.5
N2 A:ZL7401 3.6 52.7 0.5
C13 A:ZL7401 3.6 75.3 0.7
O A:HOH745 3.6 30.0 0.8
C17 A:ZL7401 3.7 43.4 0.3
CD A:GLN189 3.9 41.5 0.8
C13 A:ZL7401 4.1 40.0 0.3
CB A:MET49 4.1 41.4 1.0
CG A:MET49 4.3 43.3 1.0
OE1 A:GLN189 4.3 44.8 0.8
O A:HOH756 4.4 36.3 1.0
OG A:SER46 4.4 51.8 1.0
CA A:SER46 4.5 52.3 1.0
C17 A:ZL7401 4.5 76.2 0.7
CB A:SER46 4.5 51.5 1.0
O A:SER46 4.6 50.3 1.0
C5 A:ZL7401 4.6 76.3 0.5
C5 A:ZL7401 4.8 53.0 0.5
C14 A:ZL7401 4.8 63.9 0.7
CG A:GLN189 4.9 38.0 1.0
CB A:GLN189 4.9 32.8 1.0
C16 A:ZL7401 4.9 40.4 0.3

Fluorine binding site 6 out of 8 in 7mng

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Fluorine binding site 6 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:85.9
occ:0.50
 F3 A:ZL7401 0.0 85.9 0.5
F3 A:ZL7401 1.0 76.7 0.5
C18 A:ZL7401 1.3 86.3 0.7
C18 A:ZL7401 1.7 57.2 0.3
C11 A:ZL7401 2.0 48.8 0.5
F2 A:ZL7401 2.2 85.7 0.5
F4 A:ZL7401 2.2 85.3 0.5
C11 A:ZL7401 2.4 81.2 0.5
F2 A:ZL7401 2.5 54.9 0.5
C12 A:ZL7401 2.6 45.2 0.5
F4 A:ZL7401 2.8 54.7 0.5
C17 A:ZL7401 2.9 43.4 0.3
N2 A:ZL7401 3.4 78.6 0.5
N2 A:ZL7401 3.4 52.7 0.5
C12 A:ZL7401 3.4 80.9 0.5
OG A:SER46 3.6 51.8 1.0
NE2 A:GLN189 3.7 44.5 0.8
C13 A:ZL7401 3.7 40.0 0.3
CA A:SER46 3.7 52.3 1.0
CB A:SER46 3.8 51.5 1.0
CG A:MET49 4.0 43.3 1.0
C13 A:ZL7401 4.0 75.3 0.7
C16 A:ZL7401 4.1 40.4 0.3
CB A:MET49 4.1 41.4 1.0
O A:SER46 4.3 50.3 1.0
C5 A:ZL7401 4.4 76.3 0.5
C17 A:ZL7401 4.4 76.2 0.7
C5 A:ZL7401 4.5 53.0 0.5
O A:HOH745 4.5 30.0 0.8
C A:SER46 4.5 54.2 1.0
O A:HOH756 4.6 36.3 1.0
C14 A:ZL7401 4.7 38.2 0.3
N A:SER46 4.7 50.9 1.0
CD A:GLN189 4.7 41.5 0.8
C15 A:ZL7401 4.8 37.9 0.3
C6 A:ZL7401 4.8 103.2 0.5
O3 A:ZL7401 4.9 127.3 0.5
C6 A:ZL7401 4.9 102.8 0.5

Fluorine binding site 7 out of 8 in 7mng

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Fluorine binding site 7 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.7
occ:0.50
 F4 A:ZL7401 0.0 54.7 0.5
C18 A:ZL7401 1.3 57.2 0.3
F4 A:ZL7401 1.4 85.3 0.5
C18 A:ZL7401 1.5 86.3 0.7
F2 A:ZL7401 1.6 85.7 0.5
C11 A:ZL7401 2.1 81.2 0.5
F2 A:ZL7401 2.1 54.9 0.5
F3 A:ZL7401 2.2 76.7 0.5
N2 A:ZL7401 2.3 78.6 0.5
C11 A:ZL7401 2.4 48.8 0.5
O A:HOH745 2.6 30.0 0.8
N2 A:ZL7401 2.6 52.7 0.5
C13 A:ZL7401 2.6 75.3 0.7
C12 A:ZL7401 2.7 80.9 0.5
F3 A:ZL7401 2.8 85.9 0.5
O A:HOH662 3.1 52.4 1.0
O A:HOH756 3.3 36.3 1.0
C12 A:ZL7401 3.7 45.2 0.5
C5 A:ZL7401 3.8 76.3 0.5
O A:HOH757 3.8 49.2 1.0
C14 A:ZL7401 3.9 63.9 0.7
NE2 A:GLN189 4.0 44.5 0.8
C5 A:ZL7401 4.0 53.0 0.5
C17 A:ZL7401 4.0 76.2 0.7
C13 A:ZL7401 4.2 40.0 0.3
C6 A:ZL7401 4.4 103.2 0.5
CD A:GLN189 4.4 41.5 0.8
C6 A:ZL7401 4.5 102.8 0.5
C4 A:ZL7401 4.6 70.1 0.5
C17 A:ZL7401 4.7 43.4 0.3
OE1 A:GLN189 4.8 44.8 0.8
N1 A:ZL7401 4.8 62.0 0.5
N1 A:ZL7401 4.8 52.1 0.5
C1 A:ZL7401 4.9 57.8 0.5
C15 A:ZL7401 4.9 70.0 0.7
C4 A:ZL7401 4.9 54.4 0.5
C16 A:ZL7401 5.0 74.7 0.7

Fluorine binding site 8 out of 8 in 7mng

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Fluorine binding site 8 out of 8 in the Crystal Structure of Sars-Cov-2 Main Protease (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy)


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 (3CLPRO/Mpro) in Complex with Covalent Inhibitor Vby-825 (Partial Occupancy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:85.3
occ:0.50
 F4 A:ZL7401 0.0 85.3 0.5
C18 A:ZL7401 1.3 86.3 0.7
F4 A:ZL7401 1.4 54.7 0.5
C18 A:ZL7401 1.6 57.2 0.3
F3 A:ZL7401 1.7 76.7 0.5
F2 A:ZL7401 2.2 85.7 0.5
C11 A:ZL7401 2.2 48.8 0.5
F3 A:ZL7401 2.2 85.9 0.5
C11 A:ZL7401 2.3 81.2 0.5
N2 A:ZL7401 2.5 78.6 0.5
O A:HOH756 2.7 36.3 1.0
N2 A:ZL7401 2.7 52.7 0.5
F2 A:ZL7401 2.9 54.9 0.5
C12 A:ZL7401 3.5 80.9 0.5
O A:HOH662 3.5 52.4 1.0
C12 A:ZL7401 3.6 45.2 0.5
O A:HOH745 3.7 30.0 0.8
C5 A:ZL7401 3.7 76.3 0.5
C13 A:ZL7401 3.8 75.3 0.7
C5 A:ZL7401 4.0 53.0 0.5
C6 A:ZL7401 4.0 103.2 0.5
C6 A:ZL7401 4.1 102.8 0.5
NE2 A:GLN189 4.1 44.5 0.8
C17 A:ZL7401 4.3 43.4 0.3
C13 A:ZL7401 4.6 40.0 0.3
CD A:GLN189 4.7 41.5 0.8
C17 A:ZL7401 4.8 76.2 0.7
OE1 A:GLN189 4.8 44.8 0.8
C4 A:ZL7401 4.9 70.1 0.5
O A:HOH714 5.0 47.1 1.0
O A:HOH757 5.0 49.2 1.0
OG A:SER46 5.0 51.8 1.0

Reference:

B.Andi, D.Kumaran, D.F.Kreitler, A.S.Soares, W.Shi, J.Jakoncic, M.R.Fuchs, J.Keereetaweep, J.Shanklin, S.Mcsweeney. Hepatitis C Virus NS3/4A Inhibitors and Other Drug-Like Compounds As Efficient Covalent Binders of Sars-Cov-2 3CL Main Protease To Be Published.
Page generated: Tue Jul 15 21:48:57 2025

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