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Bromine in PDB 8dic: 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: 8dic 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) 38.46 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.346, 53.814, 115.824, 90, 100.46, 90
R / Rfree (%) 22.5 / 28.2

Other elements in 8dic:

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 8dic). 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: 8dic:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 8dic

Go back to Bromine Binding Sites List in 8dic
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:72.0
occ:0.36
 BR11 A:TNI401 0.0 72.0 0.4
C10 A:TNI401 1.9 58.1 1.0
C09 A:TNI401 2.7 65.8 1.0
C12 A:TNI401 2.9 51.4 1.0
O A:THR26 3.5 45.6 1.0
N A:THR26 3.7 43.3 1.0
CG2 A:THR25 3.7 46.6 1.0
C08 A:TNI401 4.0 62.2 1.0
CA A:THR25 4.0 52.5 1.0
N13 A:TNI401 4.1 57.5 1.0
C A:THR26 4.3 42.3 1.0
CB A:THR25 4.3 52.6 1.0
C A:THR25 4.3 45.9 1.0
C14 A:TNI401 4.5 57.2 1.0
OG1 A:THR25 4.6 52.9 1.0
CA A:THR26 4.6 42.5 1.0
O A:THR24 4.7 65.2 1.0

Bromine binding site 2 out of 4 in 8dic

Go back to Bromine Binding Sites List in 8dic
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:64.8
occ:0.24
 BR19 A:TNI401 0.0 64.8 0.2
C18 A:TNI401 2.0 63.2 1.0
C17 A:TNI401 2.7 64.3 1.0
N A:GLU166 3.2 39.6 1.0
C02 A:TNI401 3.3 60.5 1.0
CB A:MET165 3.3 43.2 1.0
CA A:MET165 3.4 36.0 1.0
C A:MET165 3.8 35.5 1.0
O A:GLU166 3.9 39.9 1.0
C05 A:TNI401 4.0 61.8 1.0
CA A:GLU166 4.2 43.3 1.0
CL01 A:TNI401 4.2 65.1 1.0
C A:GLU166 4.4 39.5 1.0
C03 A:TNI401 4.4 55.6 1.0
O A:HIS164 4.5 33.8 1.0
CB A:GLU166 4.5 39.9 1.0
N A:MET165 4.7 33.7 1.0
CG A:MET165 4.8 40.3 1.0
C04 A:TNI401 4.8 56.1 1.0
O A:HOH502 4.8 39.2 1.0
O07 A:TNI401 4.9 60.4 1.0
C06 A:TNI401 4.9 61.1 1.0
CE A:MET165 4.9 42.1 1.0

Bromine binding site 3 out of 4 in 8dic

Go back to Bromine Binding Sites List in 8dic
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:80.2
occ:0.42
 BR11 B:TNI401 0.0 80.2 0.4
C10 B:TNI401 1.9 63.3 1.0
O B:THR26 2.8 47.0 1.0
C12 B:TNI401 2.9 61.3 1.0
C09 B:TNI401 2.9 66.2 1.0
N B:THR26 3.5 59.0 1.0
C B:THR26 3.8 56.6 1.0
CG2 B:THR25 4.1 56.5 1.0
CA B:THR25 4.1 67.1 1.0
N13 B:TNI401 4.1 58.5 1.0
C08 B:TNI401 4.2 66.0 1.0
CA B:THR26 4.3 57.7 1.0
C B:THR25 4.3 62.5 1.0
CB B:THR25 4.6 65.5 1.0
C14 B:TNI401 4.7 63.8 1.0
ND2 B:ASN142 4.7 52.4 1.0
OG1 B:THR26 4.8 59.8 1.0
OG1 B:THR25 4.8 67.9 1.0
N B:LEU27 4.9 50.7 1.0

Bromine binding site 4 out of 4 in 8dic

Go back to Bromine Binding Sites List in 8dic
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:71.2
occ:0.18
 BR19 B:TNI401 0.0 71.2 0.2
C18 B:TNI401 1.9 60.6 1.0
CB B:MET165 2.4 40.8 1.0
C17 B:TNI401 2.9 60.8 1.0
C02 B:TNI401 2.9 58.5 1.0
N B:GLU166 3.0 46.3 1.0
CA B:MET165 3.0 41.6 1.0
CL01 B:TNI401 3.3 57.9 1.0
C B:MET165 3.4 40.7 1.0
O B:GLU166 3.5 44.9 1.0
CE B:MET165 3.7 54.6 1.0
CG B:MET165 3.8 45.1 1.0
CA B:GLU166 4.1 45.4 1.0
C B:GLU166 4.1 43.2 1.0
C05 B:TNI401 4.2 61.1 1.0
C03 B:TNI401 4.2 58.9 1.0
O B:HIS164 4.2 40.9 1.0
N B:MET165 4.3 35.8 1.0
SD B:MET165 4.5 63.2 1.0
O B:MET165 4.5 43.2 1.0
CB B:GLU166 4.6 43.7 1.0
C04 B:TNI401 4.7 61.2 1.0
C B:HIS164 4.7 38.7 1.0
OE1 B:GLU166 4.9 47.4 1.0

Reference:

E.A.Fink, C.Bardine, S.Gahbauer, I.Singh, K.White, S.Gu, X.Wan, B.Ary, I.Glenn, J.O'connell Iii, H.O.Donnell, P.Fajtova, J.Lyu, S.Vigneron, N.Young, C.Cohort, I.S.Kondratov, A.O.Donoghue, Y.Moroz, J.Taunton, A.Renslo, J.J.Irwin, A.G.Sastre, B.K.Shoichet, C.S.Craik. Virtual Screening For Novel Sars-Cov-2 Main Protease Non-Covalent and Covalent Inhibitors To Be Published.
Page generated: Mon Jul 7 12:10:36 2025

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