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Fluorine in PDB 7gkb: Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)

Enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)

All present enzymatic activity of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831):
3.4.22.69;

Protein crystallography data

The structure of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831), PDB code: 7gkb was solved by D.Fearon, A.Aimon, J.C.Aschenbrenner, B.H.Balcomb, F.K.R.Bertram, J.Brandao-Neto, A.Dias, A.Douangamath, L.Dunnett, A.S.Godoy, T.J.Gorrie-Stone, L.Koekemoer, T.Krojer, R.M.Lithgo, P.Lukacik, P.G.Marples, H.Mikolajek, E.Nelson, C.D.Owen, A.J.Powell, V.L.Rangel, R.Skyner, C.M.Strain-Damerell, W.Thompson, C.W.E.Tomlinson, C.Wild, M.A.Walsh, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.86 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.29, 98.74, 103.4, 90, 90, 90
R / Rfree (%) 23.9 / 28.5

Other elements in 7gkb:

The structure of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) (pdb code 7gkb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831), PDB code: 7gkb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7gkb

Go back to Fluorine Binding Sites List in 7gkb
Fluorine binding site 1 out of 4 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:42.3
occ:0.75
 F1 A:QVG408 0.0 42.3 0.8
C13 A:QVG408 1.4 42.0 0.8
C12 A:QVG408 2.3 41.9 0.8
C14 A:QVG408 2.4 41.6 0.8
CL A:QVG408 2.9 41.1 0.8
CE A:MET49 2.9 69.2 1.0
C A:ARG188 3.1 45.4 1.0
N A:ARG188 3.1 42.9 1.0
O A:ARG188 3.3 44.4 1.0
CA A:ARG188 3.4 44.2 1.0
C A:ASP187 3.5 42.3 1.0
N A:GLN189 3.5 47.8 1.0
C11 A:QVG408 3.6 41.9 0.8
C15 A:QVG408 3.6 41.5 0.8
CA A:ASP187 4.0 41.3 1.0
O A:ASP187 4.1 42.8 1.0
C16 A:QVG408 4.1 41.5 0.8
SD A:MET165 4.1 42.3 1.0
CA A:GLN189 4.2 51.1 1.0
O A:DMS403 4.3 74.6 1.0
SD A:MET49 4.5 71.0 1.0
O A:VAL186 4.6 41.5 1.0
CG A:GLN189 4.6 60.7 1.0
O1 A:QVG408 4.7 41.9 0.8
CB A:ASP187 4.8 41.0 1.0
O A:MET49 4.8 58.2 1.0
CB A:MET49 4.8 61.8 1.0
CB A:GLN189 4.8 54.1 1.0
CG A:MET49 4.8 64.8 1.0
CB A:MET165 4.9 34.8 1.0
CB A:ARG188 4.9 44.4 1.0
C1 A:DMS403 5.0 74.3 1.0

Fluorine binding site 2 out of 4 in 7gkb

Go back to Fluorine Binding Sites List in 7gkb
Fluorine binding site 2 out of 4 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:40.1
occ:0.75
 F A:QVG408 0.0 40.1 0.8
C A:QVG408 1.4 39.2 0.8
C18 A:QVG408 2.3 38.8 0.8
C1 A:QVG408 2.3 38.4 0.8
C2 A:QVG408 3.6 38.0 0.8
C17 A:QVG408 3.6 38.2 0.8
C2 A:DMS410 3.9 49.4 0.5
O A:HOH623 4.1 41.7 1.0
C3 A:QVG408 4.1 37.7 0.8
CB A:ASN142 4.1 45.3 1.0
CG A:ASN142 4.4 52.1 1.0
O A:DMS410 4.6 49.3 0.5
OD1 A:ASN142 4.6 54.2 1.0
N A:ASN142 4.6 41.0 1.0
CA A:ASN142 4.6 42.2 1.0
C6 A:QVG408 4.8 38.2 0.8
S A:DMS410 4.8 49.5 0.5
ND2 A:ASN142 4.9 53.8 1.0
N1 A:QVG408 5.0 39.2 0.8

Fluorine binding site 3 out of 4 in 7gkb

Go back to Fluorine Binding Sites List in 7gkb
Fluorine binding site 3 out of 4 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:61.9
occ:0.75
 F1 B:QVG403 0.0 61.9 0.8
C13 B:QVG403 1.3 61.7 0.8
C12 B:QVG403 2.3 61.8 0.8
C14 B:QVG403 2.3 61.4 0.8
CL B:QVG403 2.9 61.1 0.8
N B:ARG188 2.9 48.9 1.0
C B:ARG188 3.0 53.9 1.0
O B:ARG188 3.1 54.0 1.0
CA B:ARG188 3.3 51.8 1.0
C B:ASP187 3.4 46.7 1.0
N B:GLN189 3.5 55.5 1.0
C11 B:QVG403 3.6 61.9 0.8
C15 B:QVG403 3.6 61.6 0.8
O B:ASP187 4.0 47.4 1.0
CA B:ASP187 4.0 43.2 1.0
C16 B:QVG403 4.1 61.8 0.8
CA B:GLN189 4.2 56.9 1.0
O B:HOH556 4.2 56.7 1.0
SD B:MET165 4.4 52.4 1.0
O B:VAL186 4.5 39.8 1.0
O1 B:QVG403 4.7 62.0 0.8
CB B:ASP187 4.8 42.9 1.0
CB B:ARG188 4.8 54.0 1.0
NE2 B:GLN192 4.9 48.0 1.0
CB B:GLN189 4.9 59.0 1.0
CB B:MET165 4.9 38.1 1.0

Fluorine binding site 4 out of 4 in 7gkb

Go back to Fluorine Binding Sites List in 7gkb
Fluorine binding site 4 out of 4 in the Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Group Deposition Sars-Cov-2 Main Protease in Complex with Inhibitors From the Covid Moonshot -- Crystal Structure of Sars-Cov-2 Main Protease in Complex with Mat-Pos-96F51285-5 (Mpro-P0831) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:62.3
occ:0.75
 F B:QVG403 0.0 62.3 0.8
C B:QVG403 1.4 61.8 0.8
C18 B:QVG403 2.3 61.5 0.8
C1 B:QVG403 2.3 61.6 0.8
C2 B:QVG403 3.6 61.2 0.8
C17 B:QVG403 3.6 61.2 0.8
CB B:ASN142 4.1 51.5 1.0
C3 B:QVG403 4.1 60.9 0.8
CG B:ASN142 4.4 57.9 1.0
N B:ASN142 4.6 48.9 1.0
CA B:ASN142 4.6 49.3 1.0
OD1 B:ASN142 4.7 60.5 1.0
C6 B:QVG403 4.8 60.9 0.8
ND2 B:ASN142 4.9 58.8 1.0
N1 B:QVG403 5.0 61.2 0.8

Reference:

M.L.Boby, D.Fearon, M.Ferla, M.Filep, L.Koekemoer, M.C.Robinson, The Covid Moonshot Consortium, J.D.Chodera, A.A.Lee, N.London, A.Von Delft, F.Von Delft. Open Science Discovery of Potent Noncovalent Sars-Cov-2 Main Protease Inhibitors Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABO7201
Page generated: Fri Aug 2 07:39:30 2024

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