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: Fri Aug 2 09:23:03 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy