Fluorine in PDB 2gz7: Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease

The structure of Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease, PDB code: 2gz7 was solved by I.L.Lu, S.Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.776, 82.777, 53.579, 90.00, 104.93, 90.00
R / Rfree (%)	20.4 / 23.3

The structure of Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease (pdb code 2gz7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease, PDB code: 2gz7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F307 b:65.4 occ:1.00 F1 A:D3F307 0.0 65.4 1.0 C14 A:D3F307 1.3 60.7 1.0 F3 A:D3F307 2.2 61.5 1.0 F2 A:D3F307 2.2 61.2 1.0 C11 A:D3F307 2.4 62.3 1.0 O A:HOH422 2.6 54.1 1.0 C12 A:D3F307 2.7 61.4 1.0 O A:HOH553 2.9 64.8 1.0 O A:GLU166 3.6 26.9 1.0 C10 A:D3F307 3.7 68.8 1.0 C13 A:D3F307 4.1 67.6 1.0 CD2 A:LEU167 4.2 33.7 1.0 CG A:GLN192 4.2 30.1 1.0 NE2 A:GLN192 4.3 29.6 1.0 CA A:LEU167 4.4 25.1 1.0 C A:GLU166 4.5 29.4 1.0 CD A:PRO168 4.5 27.6 1.0 O A:GLN192 4.6 26.7 1.0 CD A:GLN192 4.6 29.2 1.0 O A:THR190 4.7 35.1 1.0 C9 A:D3F307 4.8 61.1 1.0 N A:LEU167 4.9 23.9 1.0 N1 A:D3F307 4.9 66.8 1.0

Fluorine binding site 2 out of 3 in the Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F307 b:61.2 occ:1.00 F2 A:D3F307 0.0 61.2 1.0 C14 A:D3F307 1.4 60.7 1.0 F3 A:D3F307 2.2 61.5 1.0 F1 A:D3F307 2.2 65.4 1.0 C11 A:D3F307 2.4 62.3 1.0 NE2 A:GLN192 2.7 29.6 1.0 C10 A:D3F307 3.0 68.8 1.0 O A:ARG188 3.2 35.9 1.0 O A:HOH553 3.4 64.8 1.0 CG A:GLN192 3.4 30.1 1.0 N A:THR190 3.5 38.2 1.0 C12 A:D3F307 3.5 61.4 1.0 CD A:GLN192 3.5 29.2 1.0 O A:THR190 3.8 35.1 1.0 CA A:GLN189 3.9 41.1 1.0 C A:ARG188 4.1 37.5 1.0 C A:GLN189 4.2 45.3 1.0 C9 A:D3F307 4.3 61.1 1.0 C A:THR190 4.4 38.5 1.0 CA A:THR190 4.5 37.2 1.0 N A:GLN189 4.5 39.6 1.0 OG1 A:THR190 4.5 53.6 1.0 O A:HOH422 4.6 54.1 1.0 C13 A:D3F307 4.7 67.6 1.0 OE1 A:GLN192 4.7 29.3 1.0 CG A:GLN189 4.9 49.2 1.0 O A:VAL186 4.9 29.8 1.0 CB A:GLN192 4.9 30.0 1.0 CB A:GLN189 4.9 40.9 1.0 CB A:THR190 5.0 43.6 1.0

Fluorine binding site 3 out of 3 in the Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Sars-Cov Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F307 b:61.5 occ:1.00 F3 A:D3F307 0.0 61.5 1.0 C14 A:D3F307 1.3 60.7 1.0 F1 A:D3F307 2.2 65.4 1.0 F2 A:D3F307 2.2 61.2 1.0 C11 A:D3F307 2.4 62.3 1.0 NE2 A:GLN192 2.7 29.6 1.0 C10 A:D3F307 2.9 68.8 1.0 CD A:GLN192 3.2 29.2 1.0 SD A:MET165 3.3 47.3 1.0 CE A:MET165 3.3 28.0 1.0 C12 A:D3F307 3.5 61.4 1.0 CG A:GLN192 3.5 30.1 1.0 CD2 A:LEU167 3.7 33.7 1.0 CB A:MET165 4.0 29.6 1.0 CG A:MET165 4.1 33.7 1.0 OE1 A:GLN192 4.1 29.3 1.0 O A:HOH553 4.2 64.8 1.0 C9 A:D3F307 4.2 61.1 1.0 O A:VAL186 4.4 29.8 1.0 O A:ARG188 4.4 35.9 1.0 O A:GLU166 4.5 26.9 1.0 C13 A:D3F307 4.6 67.6 1.0 O A:HOH422 4.7 54.1 1.0 CG A:LEU167 4.8 30.6 1.0 CB A:GLN192 4.9 30.0 1.0 C8 A:D3F307 5.0 64.0 1.0

I.L.Lu, N.Mahindroo, P.H.Liang, Y.H.Peng, C.J.Kuo, K.C.Tsai, H.P.Hsieh, Y.S.Chao, S.Y.Wu. Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Severe Acute Respiratory Syndrome Coronavirus Main Protease J.Med.Chem. V. 49 5154 2006.
ISSN: ISSN 0022-2623
PubMed: 16913704
DOI: 10.1021/JM060207O