Fluorine in PDB 7m91: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25

Enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25, PDB code: 7m91 was solved by M.G.Deshmukh, J.A.Ippolito, C.H.Zhang, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.78 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.817, 80.913, 54.546, 90, 116.58, 90
R / Rfree (%) 19.8 / 23.3

Other elements in 7m91:

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25 (pdb code 7m91). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25, PDB code: 7m91:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7m91

Go back to Fluorine Binding Sites List in 7m91
Fluorine binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.1
occ:1.00
 F1 A:YU4401 0.0 39.1 1.0
C20 A:YU4401 1.4 33.1 1.0
F2 A:YU4401 2.2 35.7 1.0
F3 A:YU4401 2.2 42.7 1.0
H14 A:YU4401 2.3 34.3 1.0
C19 A:YU4401 2.4 28.6 1.0
H13 A:YU4401 2.9 34.3 1.0
NE2 A:GLN192 3.0 24.4 1.0
CD A:GLN192 3.3 28.9 1.0
CD2 A:LEU167 3.4 20.4 1.0
CB A:GLN192 3.4 29.6 1.0
CE A:MET165 3.5 23.2 1.0
C18 A:YU4401 3.5 37.1 1.0
O4 A:YU4401 3.7 28.1 1.0
CG A:GLN192 3.7 34.6 1.0
SD A:MET165 3.9 31.0 1.0
OE1 A:GLN192 3.9 25.4 1.0
H11 A:YU4401 4.0 44.4 1.0
H12 A:YU4401 4.2 44.4 1.0
CA A:GLN192 4.6 37.4 1.0
O A:ARG188 4.7 28.3 1.0
C17 A:YU4401 4.7 29.0 1.0
O A:THR190 4.8 45.2 1.0
O A:GLN192 4.8 38.1 1.0
H15 A:YU4401 4.8 30.6 1.0
CG A:LEU167 4.8 26.3 1.0
CB A:MET165 4.9 19.9 1.0
O A:VAL186 4.9 22.4 1.0
N A:GLN192 4.9 42.3 1.0
O A:GLU166 4.9 20.1 1.0
CA A:LEU167 4.9 18.7 1.0
C A:GLN192 5.0 39.8 1.0

Fluorine binding site 2 out of 3 in 7m91

Go back to Fluorine Binding Sites List in 7m91
Fluorine binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.7
occ:1.00
 F2 A:YU4401 0.0 35.7 1.0
C20 A:YU4401 1.4 33.1 1.0
F1 A:YU4401 2.2 39.1 1.0
F3 A:YU4401 2.2 42.7 1.0
H13 A:YU4401 2.4 34.3 1.0
C19 A:YU4401 2.4 28.6 1.0
H14 A:YU4401 3.1 34.3 1.0
H11 A:YU4401 3.3 44.4 1.0
C18 A:YU4401 3.4 37.1 1.0
CD A:PRO168 3.5 27.6 1.0
O A:GLN192 3.8 38.1 1.0
O A:THR190 3.8 45.2 1.0
CB A:GLN192 3.8 29.6 1.0
O4 A:YU4401 4.0 28.1 1.0
CG A:PRO168 4.0 27.3 1.0
CD2 A:LEU167 4.1 20.4 1.0
N A:GLN192 4.2 42.3 1.0
H12 A:YU4401 4.2 44.4 1.0
CA A:GLN192 4.4 37.4 1.0
C A:GLN192 4.4 39.8 1.0
CG A:GLN192 4.4 34.6 1.0
CA A:LEU167 4.5 18.7 1.0
NE2 A:GLN189 4.5 44.7 1.0
NE2 A:GLN192 4.5 24.4 1.0
N A:PRO168 4.6 25.4 1.0
O A:GLU166 4.6 20.1 1.0
CD A:GLN192 4.7 28.9 1.0
C A:THR190 5.0 49.2 1.0
C A:LEU167 5.0 22.0 1.0

Fluorine binding site 3 out of 3 in 7m91

Go back to Fluorine Binding Sites List in 7m91
Fluorine binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 25 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.7
occ:1.00
 F3 A:YU4401 0.0 42.7 1.0
C20 A:YU4401 1.4 33.1 1.0
F1 A:YU4401 2.2 39.1 1.0
F2 A:YU4401 2.2 35.7 1.0
O4 A:YU4401 2.3 28.1 1.0
C19 A:YU4401 2.3 28.6 1.0
C18 A:YU4401 2.5 37.1 1.0
H11 A:YU4401 2.6 44.4 1.0
H14 A:YU4401 2.9 34.3 1.0
H13 A:YU4401 3.1 34.3 1.0
H12 A:YU4401 3.4 44.4 1.0
C17 A:YU4401 3.6 29.0 1.0
O A:ARG188 3.6 28.3 1.0
NE2 A:GLN192 3.6 24.4 1.0
NE2 A:GLN189 3.6 44.7 1.0
O A:THR190 3.7 45.2 1.0
H15 A:YU4401 3.7 30.6 1.0
OE1 A:GLN189 3.9 49.8 1.0
CD A:GLN189 4.0 49.2 1.0
N A:THR190 4.1 50.2 1.0
C21 A:YU4401 4.1 25.6 1.0
CA A:GLN189 4.2 43.6 1.0
CD A:GLN192 4.4 28.9 1.0
C A:ARG188 4.5 35.0 1.0
CG A:GLN192 4.5 34.6 1.0
SD A:MET165 4.6 31.0 1.0
CB A:GLN192 4.7 29.6 1.0
C A:GLN189 4.7 51.4 1.0
C16 A:YU4401 4.7 24.3 1.0
C A:THR190 4.7 49.2 1.0
H10 A:YU4401 4.8 29.1 1.0
N A:GLN189 4.9 42.0 1.0
CE A:MET165 5.0 23.2 1.0

Reference:

M.G.Deshmukh, J.A.Ippolito, C.-H.Zhang, E.A.Stone, R.A.Reilly, S.J.Miller, W.L.Jorgensen, K.S.Anderson. Structure-Guided Design of A Perampanel-Derived Pharmacophore Targeting the Sars-Cov-2 Main Protease Structure 2021.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2021.06.002
Page generated: Sat Jul 10 14:26:10 2021

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