Atomistry » Bromine » PDB 8cco-8eyd » 8did
Atomistry »
  Bromine »
    PDB 8cco-8eyd »
      8did »

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: Thu Jul 11 05:03:24 2024

Last articles

Cl in 4NHT
Cl in 4NO7
Cl in 4NML
Cl in 4NN3
Cl in 4NMW
Cl in 4NM7
Cl in 4NM5
Cl in 4NM3
Cl in 4NM0
Cl in 4NHQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy