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Fluorine in PDB 8ur9: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61, PDB code: 8ur9 was solved by C.Papini, 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) 56.91 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.91, 99.895, 104.314, 90, 90, 90
R / Rfree (%) 20.4 / 23.6

Other elements in 8ur9:

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61 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 Main Protease in Complex with Compound 61 (pdb code 8ur9). 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 Main Protease in Complex with Compound 61, PDB code: 8ur9:

Fluorine binding site 1 out of 1 in 8ur9

Go back to Fluorine Binding Sites List in 8ur9
Fluorine binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with Compound 61


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 Main Protease in Complex with Compound 61 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:71.3
occ:1.00
 F1 A:XEK401 0.0 71.3 1.0
C6 A:XEK401 1.4 67.0 1.0
C5 A:XEK401 2.4 62.8 1.0
C7 A:XEK401 2.4 69.0 1.0
O2 A:XEK401 2.8 79.5 1.0
CL1 A:XEK401 3.0 70.9 1.0
C A:ARG188 3.2 58.1 1.0
N A:GLN189 3.3 59.6 1.0
O A:ARG188 3.3 55.4 1.0
CA A:GLN189 3.6 67.2 1.0
C4 A:XEK401 3.6 53.6 1.0
C15 A:XEK401 3.6 64.4 1.0
H3 A:XEK401 3.7 97.7 1.0
N A:ARG188 3.7 55.1 1.0
C8 A:XEK401 3.8 81.4 1.0
CA A:ARG188 3.9 57.8 1.0
CB A:GLN189 4.1 74.9 1.0
C3 A:XEK401 4.1 54.0 1.0
C A:ASP187 4.1 53.6 1.0
CE A:MET49 4.3 74.1 1.0
SD A:MET165 4.3 57.7 1.0
CG A:GLN189 4.4 79.4 1.0
H1 A:XEK401 4.5 64.4 1.0
H8 A:XEK401 4.5 77.2 1.0
CL2 A:XEK401 4.6 94.2 1.0
C9 A:XEK401 4.6 82.9 1.0
SD A:MET49 4.6 92.2 1.0
O A:ASP187 4.6 52.7 1.0
CA A:ASP187 4.6 43.2 1.0
H2 A:XEK401 4.7 97.7 1.0
CD A:GLN189 4.9 85.8 1.0
C14 A:XEK401 4.9 84.1 1.0
NE2 A:GLN189 4.9 85.0 1.0
C A:GLN189 5.0 71.3 1.0
CB A:MET165 5.0 41.7 1.0

Reference:

C.Papini, I.Ullah, A.P.Ranjan, S.Zhang, Q.Wu, K.A.Spasov, C.Zhang, W.Mothes, J.M.Crawford, B.D.Lindenbach, P.D.Uchil, P.Kumar, W.L.Jorgensen, K.S.Anderson. Proof-of-Concept Studies with A Computationally Designed M Pro Inhibitor As A Synergistic Combination Regimen Alternative to Paxlovid. Proc.Natl.Acad.Sci.Usa V. 121 13121 2024.
ISSN: ESSN 1091-6490
PubMed: 38621119
DOI: 10.1073/PNAS.2320713121
Page generated: Wed Jul 16 09:24:33 2025

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