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Fluorine in PDB 7b2u: Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1, PDB code: 7b2u was solved by V.O.Talibov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.517, 53.682, 114.508, 90, 100.59, 90
R / Rfree (%) 20.8 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1 (pdb code 7b2u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1, PDB code: 7b2u:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7b2u

Go back to Fluorine Binding Sites List in 7b2u
Fluorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1


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 Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.6
occ:1.00
F1 A:SQ5401 0.0 35.6 1.0
C14 A:SQ5401 1.4 36.3 1.0
C15 A:SQ5401 2.4 29.1 1.0
C13 A:SQ5401 2.4 29.8 1.0
O A:HOH676 3.3 41.0 1.0
O A:PHE140 3.3 26.8 1.0
OE2 A:GLU166 3.4 29.3 1.0
N B:SER1 3.5 31.0 1.0
O B:HOH599 3.5 40.0 1.0
N A:ASN142 3.5 32.2 1.0
C A:LEU141 3.6 29.6 1.0
N3 A:SQ5401 3.6 28.1 1.0
C11 A:SQ5401 3.6 31.2 1.0
CA A:LEU141 3.6 29.6 1.0
CD A:GLU166 4.0 35.4 1.0
C12 A:SQ5401 4.0 25.2 1.0
C A:PHE140 4.1 23.8 1.0
O A:LEU141 4.2 25.6 1.0
N A:LEU141 4.3 28.4 1.0
OE1 A:GLU166 4.4 45.4 1.0
CA A:ASN142 4.4 23.6 1.0
CB A:GLU166 4.5 22.3 1.0
N2 A:SQ5401 4.8 29.5 1.0
CG A:GLU166 4.8 27.0 1.0
CB A:LEU141 4.8 30.8 1.0
CA B:SER1 4.9 33.5 1.0
CB A:ASN142 5.0 33.1 1.0

Fluorine binding site 2 out of 2 in 7b2u

Go back to Fluorine Binding Sites List in 7b2u
Fluorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1


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 Sars-Cov-2 Main Protease (NSP5) in Complex with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:36.8
occ:1.00
F1 B:SQ5401 0.0 36.8 1.0
C14 B:SQ5401 1.4 33.1 1.0
C15 B:SQ5401 2.4 27.2 1.0
C13 B:SQ5401 2.4 29.2 1.0
O B:HOH697 3.3 44.9 1.0
N A:SER1 3.3 30.2 1.0
O B:HOH644 3.3 40.5 1.0
O B:PHE140 3.3 27.6 1.0
OE2 B:GLU166 3.5 27.0 1.0
O A:HOH528 3.5 39.4 1.0
N B:ASN142 3.6 31.2 1.0
C B:LEU141 3.6 25.4 1.0
N3 B:SQ5401 3.6 26.2 1.0
C11 B:SQ5401 3.6 26.3 1.0
CA B:LEU141 3.7 27.8 1.0
C12 B:SQ5401 4.1 21.1 1.0
CD B:GLU166 4.1 33.0 1.0
C B:PHE140 4.1 26.1 1.0
O B:LEU141 4.2 26.0 1.0
N B:LEU141 4.3 27.5 1.0
CA B:ASN142 4.3 25.2 1.0
CB B:GLU166 4.5 20.8 1.0
OE1 B:GLU166 4.6 39.6 1.0
CA A:SER1 4.7 31.3 1.0
N2 B:SQ5401 4.8 28.6 1.0
CG B:GLU166 4.9 25.2 1.0
CB B:LEU141 4.9 24.1 1.0
CB B:ASN142 4.9 33.9 1.0

Reference:

A.Luttens, H.Gullberg, E.Abdurakhmanov, D.D.Vo, D.Akaberi, V.O.Talibov, N.Nekhotiaeva, L.Vangeel, S.De Jonghe, D.Jochmans, J.Krambrich, A.Tas, B.Lundgren, Y.Gravenfors, A.J.Craig, Y.Atilaw, A.Sandstrom, L.W.K.Moodie, A.Lundkvist, M.J.Van Hemert, J.Neyts, J.Lennerstrand, J.Kihlberg, K.Sandberg, U.H.Danielson, J.Carlsson. Ultralarge Virtual Screening Identifies Sars-Cov-2 Main Protease Inhibitors with Broad-Spectrum Activity Against Coronaviruses. J.Am.Chem.Soc. V. 144 2905 2022.
ISSN: ESSN 1520-5126
PubMed: 35142215
DOI: 10.1021/JACS.1C08402
Page generated: Fri Aug 2 05:54:25 2024

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