Bromine in PDB 8did: Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors

Enzymatic activity of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors

All present enzymatic activity of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors:
3.4.22.69;

Protein crystallography data

The structure of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors, PDB code: 8did was solved by I.Singh, B.K.Shoichet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.22 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.238, 53.666, 115.632, 90, 100.94, 90
R / Rfree (%) 25.4 / 29.4

Other elements in 8did:

The structure of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors (pdb code 8did). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors, PDB code: 8did:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 8did

Go back to Bromine Binding Sites List in 8did
Bromine binding site 1 out of 4 in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:92.5
occ:1.00
 BR06 A:U0R401 0.0 92.5 1.0
C05 A:U0R401 2.0 45.8 1.0
C07 A:U0R401 3.0 49.8 1.0
C04 A:U0R401 3.0 52.8 1.0
CA A:ASP187 3.3 25.2 1.0
CD2 A:HIS41 3.4 29.1 1.0
CB A:ASP187 3.4 22.2 1.0
O A:HIS164 3.4 30.9 1.0
CB A:MET165 3.7 35.6 1.0
C A:ASP187 3.7 29.1 1.0
N A:ARG188 3.9 30.6 1.0
NE2 A:HIS41 4.0 32.3 1.0
CE A:MET165 4.1 31.1 1.0
C A:HIS164 4.2 27.5 1.0
CG A:HIS41 4.2 32.8 1.0
SD A:MET165 4.2 49.5 1.0
C03 A:U0R401 4.3 54.2 1.0
C08 A:U0R401 4.3 52.4 1.0
CG A:MET165 4.4 33.3 1.0
O A:ASP187 4.4 26.9 1.0
CB A:HIS164 4.6 28.8 1.0
O A:VAL186 4.6 31.0 1.0
N A:ASP187 4.6 26.7 1.0
CA A:MET165 4.6 27.6 1.0
O A:HOH516 4.7 23.1 1.0
CB A:HIS41 4.7 28.8 1.0
C02 A:U0R401 4.8 55.4 1.0
N A:MET165 4.8 24.3 1.0
CA A:ARG188 4.9 34.8 1.0
CG A:ASP187 4.9 25.1 1.0
CZ A:PHE181 4.9 26.3 1.0
O A:ARG188 4.9 32.0 1.0
C A:ARG188 5.0 35.5 1.0
CA A:HIS164 5.0 24.5 1.0
CE1 A:HIS41 5.0 33.0 1.0

Bromine binding site 2 out of 4 in 8did

Go back to Bromine Binding Sites List in 8did
Bromine binding site 2 out of 4 in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:109.5
occ:1.00
 BR14 A:U0R401 0.0 109.5 1.0
C13 A:U0R401 1.9 53.5 1.0
C15 A:U0R401 2.9 48.0 1.0
C12 A:U0R401 2.9 46.8 1.0
O A:THR26 3.3 37.4 1.0
N16 A:U0R401 4.1 43.7 1.0
OD1 A:ASN142 4.2 41.7 1.0
C11 A:U0R401 4.2 48.6 1.0
N A:THR26 4.3 38.7 1.0
CG2 A:THR25 4.3 40.4 1.0
C A:THR26 4.4 33.7 1.0
ND2 A:ASN142 4.5 43.1 1.0
C17 A:U0R401 4.7 46.9 1.0
CG A:ASN142 4.7 39.1 1.0
CA A:THR25 4.9 39.5 1.0
CA A:THR26 5.0 39.6 1.0

Bromine binding site 3 out of 4 in 8did

Go back to Bromine Binding Sites List in 8did
Bromine binding site 3 out of 4 in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:92.5
occ:1.00
 BR06 B:U0R401 0.0 92.5 1.0
C05 B:U0R401 2.0 45.8 1.0
C07 B:U0R401 3.0 49.8 1.0
C04 B:U0R401 3.0 52.8 1.0
CB B:ASP187 3.3 22.7 1.0
CA B:ASP187 3.3 25.4 1.0
CE B:MET49 3.3 30.1 1.0
CD2 B:HIS41 3.5 29.8 1.0
O B:HIS164 3.5 26.5 1.0
C B:ASP187 3.6 26.1 1.0
SD B:MET165 3.7 41.7 1.0
CB B:MET165 3.7 33.4 1.0
N B:ARG188 3.9 31.2 1.0
NE2 B:HIS41 4.2 28.6 1.0
O B:ASP187 4.2 24.4 1.0
C03 B:U0R401 4.3 54.2 1.0
C B:HIS164 4.3 22.1 1.0
C08 B:U0R401 4.3 52.4 1.0
CG B:MET165 4.3 27.2 1.0
CG B:HIS41 4.3 24.8 1.0
CE B:MET165 4.3 36.3 1.0
CB B:HIS164 4.5 18.6 1.0
O B:HOH526 4.6 17.6 1.0
N B:ASP187 4.6 19.2 1.0
CB B:HIS41 4.7 23.1 1.0
CG B:ASP187 4.7 23.9 1.0
CA B:MET165 4.7 29.3 1.0
O B:VAL186 4.7 27.6 1.0
SD B:MET49 4.8 45.9 1.0
C02 B:U0R401 4.8 55.4 1.0
CA B:ARG188 4.8 31.1 1.0
CZ B:PHE181 4.9 20.9 1.0
N B:MET165 4.9 22.3 1.0
OH B:TYR54 5.0 25.0 1.0
CA B:HIS164 5.0 21.5 1.0

Bromine binding site 4 out of 4 in 8did

Go back to Bromine Binding Sites List in 8did
Bromine binding site 4 out of 4 in the Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:109.5
occ:1.00
 BR14 B:U0R401 0.0 109.5 1.0
C13 B:U0R401 1.9 53.5 1.0
C15 B:U0R401 2.9 48.0 1.0
C12 B:U0R401 2.9 46.8 1.0
O B:THR26 3.5 34.0 1.0
N16 B:U0R401 4.1 43.7 1.0
CG2 B:THR25 4.1 38.3 1.0
C11 B:U0R401 4.2 48.6 1.0
N B:THR26 4.2 36.4 1.0
OD1 B:ASN142 4.4 50.1 1.0
C B:THR26 4.5 33.1 1.0
C17 B:U0R401 4.7 46.9 1.0
CA B:THR25 4.7 40.7 1.0
C B:THR25 5.0 38.7 1.0
CB B:THR25 5.0 40.7 1.0

Reference:

E.A.Fink, C.Bardine, S.Gahbauer, I.Singh, T.Detomasi, K.White, S.Gu, X.Wan, J.Chen, B.Ary, I.Glenn, J.O'connell, H.O'donnell, P.Fajtova, J.Lyu, S.Vigneron, N.J.Young, I.S.Kondratov, A.Alisoltani, L.M.Simons, R.Lorenzo-Redondo, E.A.Ozer, J.F.Hultquist, A.J.O'donoghue, Y.Moroz, J.Taunton, A.R.Renslo, J.J.Irwin, A.Garcia-Sastre, B.K.Shoichet, C.S.Craik. Large Library Docking For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors. Protein Sci. E4712 2023.
ISSN: ESSN 1469-896X
PubMed: 37354015
DOI: 10.1002/PRO.4712
Page generated: Wed Jul 26 11:53:42 2023

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