Fluorine in PDB 8v4u: Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor

Enzymatic activity of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor:
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor, PDB code: 8v4u was solved by S.E.Greasley, R.A.Ferre, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.69 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.407, 54.138, 115.15, 90, 101.86, 90
R / Rfree (%) 21.6 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor (pdb code 8v4u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor, PDB code: 8v4u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 1 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.8
occ:1.00
 F1 A:YDL401 0.0 34.8 1.0
C21 A:YDL401 1.4 34.8 1.0
F3 A:YDL401 2.2 35.3 1.0
F2 A:YDL401 2.3 34.4 1.0
C11 A:YDL401 2.3 34.4 1.0
H15 A:YDL401 2.5 33.7 0.0
H13 A:YDL401 2.6 34.4 0.0
C12 A:YDL401 2.9 33.7 1.0
ND1 A:HIS41 3.4 24.1 1.0
CB A:HIS41 3.5 21.8 1.0
O A:ASP187 3.5 21.1 1.0
CG A:HIS41 3.6 22.2 1.0
C A:ASP187 3.6 20.8 1.0
H14 A:YDL401 3.6 33.7 0.0
SD A:MET49 3.7 46.0 1.0
C10 A:YDL401 3.7 34.2 1.0
CB A:ASP187 3.8 20.7 1.0
OH A:TYR54 3.8 25.5 1.0
H12 A:YDL401 3.8 34.2 0.0
CA A:ASP187 3.9 20.2 1.0
C8 A:YDL401 4.0 33.5 1.0
H9 A:YDL401 4.0 33.5 0.0
N A:ARG188 4.1 21.1 1.0
CE1 A:HIS41 4.2 23.6 1.0
H11 A:YDL401 4.4 34.2 0.0
CD2 A:HIS41 4.5 22.6 1.0
N3 A:YDL401 4.5 33.8 1.0
CE A:MET49 4.6 46.4 1.0
CA A:ARG188 4.6 22.5 1.0
NE2 A:HIS41 4.8 23.7 1.0
O A:HOH518 4.8 17.2 1.0
CG A:ASP187 4.9 23.1 1.0
C A:ARG188 4.9 22.9 1.0

Fluorine binding site 2 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 2 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.4
occ:1.00
 F2 A:YDL401 0.0 34.4 1.0
C21 A:YDL401 1.4 34.8 1.0
F3 A:YDL401 2.2 35.3 1.0
F1 A:YDL401 2.3 34.8 1.0
C11 A:YDL401 2.4 34.4 1.0
H12 A:YDL401 2.6 34.2 0.0
H9 A:YDL401 2.7 33.5 0.0
H15 A:YDL401 2.9 33.7 0.0
C10 A:YDL401 2.9 34.2 1.0
C12 A:YDL401 3.0 33.7 1.0
C8 A:YDL401 3.1 33.5 1.0
H13 A:YDL401 3.3 34.4 0.0
N3 A:YDL401 3.4 33.8 1.0
CB A:MET165 3.4 21.5 1.0
SD A:MET165 3.6 37.4 1.0
H11 A:YDL401 3.9 34.2 0.0
CA A:ASP187 4.0 20.2 1.0
H14 A:YDL401 4.0 33.7 0.0
C13 A:YDL401 4.1 33.5 1.0
C A:ASP187 4.1 20.8 1.0
O A:HIS164 4.1 19.1 1.0
N A:ARG188 4.1 21.1 1.0
CG A:MET165 4.1 25.2 1.0
ND1 A:HIS41 4.3 24.1 1.0
CB A:ASP187 4.3 20.7 1.0
O3 A:YDL401 4.5 32.9 1.0
CE1 A:HIS41 4.6 23.6 1.0
C9 A:YDL401 4.6 33.0 1.0
C A:ARG188 4.6 22.9 1.0
CA A:MET165 4.6 19.9 1.0
O A:ARG188 4.7 22.0 1.0
O A:ASP187 4.7 21.1 1.0
H16 A:YDL401 4.8 33.2 0.0
H10 A:YDL401 4.8 32.1 0.0
H25 A:YDL401 4.8 33.4 0.0
C18 A:YDL401 4.8 34.1 1.0
C A:HIS164 4.8 18.6 1.0
O4 A:YDL401 4.9 34.8 1.0
CA A:ARG188 4.9 22.5 1.0
O A:VAL186 4.9 20.6 1.0
C14 A:YDL401 4.9 33.2 1.0
CE A:MET165 4.9 36.8 1.0
N A:GLN189 4.9 23.8 1.0
N4 A:YDL401 4.9 33.7 1.0

Fluorine binding site 3 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 3 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.3
occ:1.00
 F3 A:YDL401 0.0 35.3 1.0
C21 A:YDL401 1.4 34.8 1.0
F2 A:YDL401 2.2 34.4 1.0
F1 A:YDL401 2.2 34.8 1.0
C11 A:YDL401 2.4 34.4 1.0
H12 A:YDL401 2.5 34.2 0.0
H13 A:YDL401 2.7 34.4 0.0
C10 A:YDL401 2.9 34.2 1.0
C A:ARG188 2.9 22.9 1.0
N A:GLN189 3.0 23.8 1.0
N A:ARG188 3.1 21.1 1.0
CA A:ARG188 3.2 22.5 1.0
C A:ASP187 3.3 20.8 1.0
O A:ARG188 3.4 22.0 1.0
H11 A:YDL401 3.5 34.2 0.0
O A:ASP187 3.7 21.1 1.0
CA A:GLN189 3.7 24.6 1.0
C12 A:YDL401 3.8 33.7 1.0
H15 A:YDL401 4.0 33.7 0.0
CB A:GLN189 4.0 25.9 1.0
CA A:ASP187 4.1 20.2 1.0
N3 A:YDL401 4.1 33.8 1.0
O A:MET49 4.2 29.6 1.0
C8 A:YDL401 4.4 33.5 1.0
H9 A:YDL401 4.5 33.5 0.0
SD A:MET49 4.5 46.0 1.0
O4 A:YDL401 4.5 34.8 1.0
H14 A:YDL401 4.5 33.7 0.0
CB A:ASP187 4.7 20.7 1.0
H25 A:YDL401 4.7 33.4 0.0
CB A:ARG188 4.7 24.0 1.0
H16 A:YDL401 4.7 33.2 0.0
CB A:MET49 4.8 33.4 1.0
O A:VAL186 5.0 20.6 1.0

Fluorine binding site 4 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 4 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:36.6
occ:1.00
 F1 B:YDL401 0.0 36.6 1.0
C21 B:YDL401 1.4 36.2 1.0
F3 B:YDL401 2.2 36.4 1.0
F2 B:YDL401 2.2 35.2 1.0
C11 B:YDL401 2.4 35.3 1.0
H13 B:YDL401 2.6 35.3 0.0
H15 B:YDL401 2.7 34.7 0.0
C12 B:YDL401 3.0 34.7 1.0
O B:ASP187 3.3 18.1 1.0
C B:ASP187 3.4 18.8 1.0
CB B:HIS41 3.6 23.7 1.0
ND1 B:HIS41 3.6 27.1 1.0
CB B:ASP187 3.6 18.9 1.0
CA B:ASP187 3.7 18.3 1.0
C10 B:YDL401 3.7 34.5 1.0
CG B:HIS41 3.8 25.0 1.0
H14 B:YDL401 3.8 34.7 0.0
H12 B:YDL401 3.8 34.5 0.0
OH B:TYR54 3.8 23.5 1.0
SD B:MET49 3.8 49.8 1.0
N B:ARG188 3.9 19.7 1.0
H9 B:YDL401 4.0 34.1 0.0
C8 B:YDL401 4.1 34.1 1.0
CE1 B:HIS41 4.4 27.2 1.0
H11 B:YDL401 4.4 34.5 0.0
CA B:ARG188 4.5 21.3 1.0
CE B:MET49 4.5 49.7 1.0
N3 B:YDL401 4.5 33.4 1.0
CD2 B:HIS41 4.6 25.6 1.0
O B:HOH550 4.8 15.1 1.0
C B:ARG188 4.8 22.8 1.0
CG B:ASP187 4.8 23.4 1.0
NE2 B:HIS41 5.0 27.0 1.0

Fluorine binding site 5 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 5 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:35.2
occ:1.00
 F2 B:YDL401 0.0 35.2 1.0
C21 B:YDL401 1.4 36.2 1.0
F3 B:YDL401 2.2 36.4 1.0
F1 B:YDL401 2.2 36.6 1.0
C11 B:YDL401 2.4 35.3 1.0
H12 B:YDL401 2.6 34.5 0.0
H9 B:YDL401 2.7 34.1 0.0
C10 B:YDL401 2.9 34.5 1.0
H15 B:YDL401 2.9 34.7 0.0
C12 B:YDL401 3.0 34.7 1.0
C8 B:YDL401 3.1 34.1 1.0
N3 B:YDL401 3.2 33.4 1.0
CB B:MET165 3.3 26.2 1.0
H13 B:YDL401 3.3 35.3 0.0
SD B:MET165 3.7 38.5 1.0
C13 B:YDL401 3.9 31.9 1.0
H11 B:YDL401 3.9 34.5 0.0
H14 B:YDL401 4.0 34.7 0.0
CA B:ASP187 4.1 18.3 1.0
CG B:MET165 4.1 29.6 1.0
C B:ASP187 4.2 18.8 1.0
N B:ARG188 4.2 19.7 1.0
O B:HIS164 4.2 22.8 1.0
O3 B:YDL401 4.3 31.4 1.0
CA B:MET165 4.4 24.5 1.0
CB B:ASP187 4.5 18.9 1.0
ND1 B:HIS41 4.5 27.1 1.0
C18 B:YDL401 4.5 31.5 1.0
H16 B:YDL401 4.6 30.7 0.0
C9 B:YDL401 4.6 33.6 1.0
O4 B:YDL401 4.6 31.6 1.0
N4 B:YDL401 4.7 30.7 1.0
C14 B:YDL401 4.7 30.7 1.0
O B:ARG188 4.7 21.8 1.0
H10 B:YDL401 4.7 32.8 0.0
C B:ARG188 4.7 22.8 1.0
O B:ASP187 4.8 18.1 1.0
CE B:MET165 4.8 38.8 1.0
O B:VAL186 4.8 20.2 1.0
C B:HIS164 4.8 22.7 1.0
CE1 B:HIS41 4.8 27.2 1.0
N B:MET165 4.9 23.7 1.0
CA B:ARG188 5.0 21.3 1.0
H25 B:YDL401 5.0 32.5 0.0
O5 B:YDL401 5.0 32.2 1.0

Fluorine binding site 6 out of 6 in 8v4u

Go back to Fluorine Binding Sites List in 8v4u
Fluorine binding site 6 out of 6 in the Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Sars-Cov-2 Main Protease in Complex with A Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:36.4
occ:1.00
 F3 B:YDL401 0.0 36.4 1.0
C21 B:YDL401 1.4 36.2 1.0
F1 B:YDL401 2.2 36.6 1.0
F2 B:YDL401 2.2 35.2 1.0
C11 B:YDL401 2.4 35.3 1.0
H12 B:YDL401 2.4 34.5 0.0
H13 B:YDL401 2.6 35.3 0.0
C10 B:YDL401 2.9 34.5 1.0
C B:ARG188 3.0 22.8 1.0
N B:ARG188 3.1 19.7 1.0
N B:GLN189 3.1 23.9 1.0
CA B:ARG188 3.2 21.3 1.0
C B:ASP187 3.3 18.8 1.0
O B:ARG188 3.4 21.8 1.0
H11 B:YDL401 3.5 34.5 0.0
O B:ASP187 3.7 18.1 1.0
C12 B:YDL401 3.8 34.7 1.0
CA B:GLN189 3.8 25.6 1.0
H15 B:YDL401 4.0 34.7 0.0
CB B:GLN189 4.0 26.3 1.0
N3 B:YDL401 4.0 33.4 1.0
CA B:ASP187 4.1 18.3 1.0
O4 B:YDL401 4.2 31.6 1.0
SD B:MET49 4.4 49.8 1.0
C8 B:YDL401 4.4 34.1 1.0
O B:MET49 4.4 31.4 1.0
H9 B:YDL401 4.4 34.1 0.0
H14 B:YDL401 4.5 34.7 0.0
H16 B:YDL401 4.6 30.7 0.0
C18 B:YDL401 4.7 31.5 1.0
CB B:ARG188 4.8 23.0 1.0
CB B:MET49 4.8 35.9 1.0
CB B:ASP187 4.8 18.9 1.0
H25 B:YDL401 4.8 32.5 0.0
O B:VAL186 4.9 20.2 1.0
C13 B:YDL401 4.9 31.9 1.0

Reference:

C.M.N.Allerton, J.T.Arcari, L.M.Aschenbrenner, M.Avery, B.M.Bechle, M.A.Behzadi, B.Boras, L.M.Buzon, R.D.Cardin, N.R.Catlin, A.A.Carlo, K.J.Coffman, A.Dantonio, L.Di, H.Eng, K.A.Farley, R.A.Ferre, S.S.Gernhardt, S.A.Gibson, S.E.Greasley, S.R.Greenfield, B.L.Hurst, A.S.Kalgutkar, E.Kimoto, L.F.Lanyon, G.H.Lovett, Y.Lian, W.Liu, L.A.Martinez Alsina, S.Noell, R.S.Obach, D.R.Owen, N.C.Patel, D.K.Rai, M.R.Reese, H.A.Rothan, S.Sakata, M.F.Sammons, J.G.Sathish, R.Sharma, C.M.Steppan, J.B.Tuttle, P.R.Verhoest, L.Wei, Q.Yang, I.Yurgelonis, Y.Zhu. A Second-Generation Oral Sars-Cov-2 Main Protease Inhibitor Clinical Candidate For the Treatment of Covid-19. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38687966
DOI: 10.1021/ACS.JMEDCHEM.3C02469
Page generated: Sat Aug 3 01:18:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy