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Fluorine in PDB 7m8p: Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23

Enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23

All present enzymatic activity of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23:
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 23, PDB code: 7m8p 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) 72.43 / 2.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.181, 100.606, 104.355, 90, 90, 90
R / Rfree (%) 18.5 / 23.1

Other elements in 7m8p:

The structure of Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 23 (pdb code 7m8p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23, PDB code: 7m8p:

Fluorine binding site 1 out of 1 in 7m8p

Go back to Fluorine Binding Sites List in 7m8p
Fluorine binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2(2019-Ncov) Main Protease in Complex with Compound 23


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 23 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.7
occ:1.00
 F1 A:YSJ401 0.0 54.7 1.0
C27 A:YSJ401 1.4 55.1 1.0
C1 A:YSJ401 2.3 50.4 1.0
C19 A:YSJ401 2.4 56.0 1.0
CL1 A:YSJ401 2.8 58.7 1.0
O4 A:YSJ401 2.9 60.7 1.0
C A:ARG188 3.1 45.5 1.0
N A:GLN189 3.2 40.6 1.0
O A:ARG188 3.3 41.1 1.0
CG A:GLN189 3.4 61.0 1.0
CA A:ARG188 3.5 43.2 1.0
N A:ARG188 3.6 42.7 1.0
C2 A:YSJ401 3.6 43.0 1.0
C18 A:YSJ401 3.7 53.9 1.0
CA A:GLN189 3.7 48.0 1.0
CL2 A:YSJ401 4.1 74.9 1.0
C20 A:YSJ401 4.1 58.0 1.0
C3 A:YSJ401 4.1 43.0 1.0
SD A:MET165 4.1 49.8 1.0
CB A:GLN189 4.1 52.2 1.0
C A:ASP187 4.1 42.1 1.0
H13 A:YSJ401 4.1 69.6 1.0
H1 A:YSJ401 4.5 51.6 1.0
H11 A:YSJ401 4.5 64.7 1.0
CA A:ASP187 4.6 39.4 1.0
C21 A:YSJ401 4.7 55.7 1.0
C22 A:YSJ401 4.7 55.7 1.0
CD A:GLN189 4.7 65.0 1.0
O A:ASP187 4.8 38.8 1.0
H12 A:YSJ401 4.9 69.6 1.0
NE2 A:GLN189 4.9 62.4 1.0
O A:VAL186 4.9 39.4 1.0
CB A:ARG188 5.0 46.9 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: Tue Jul 15 21:34:54 2025

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