Fluorine in PDB 2gz8: 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: 2gz8 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 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.279, 82.107, 53.407, 90.00, 104.66, 90.00
R / Rfree (%)	21.5 / 24.1

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 2gz8). 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: 2gz8:
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:55.7 occ:1.00 FAW A:F3F307 0.0 55.7 1.0 CAU A:F3F307 1.3 61.9 1.0 FAX A:F3F307 2.2 58.1 1.0 FAV A:F3F307 2.2 58.7 1.0 CAS A:F3F307 2.4 68.2 1.0 NAR A:F3F307 3.0 61.1 1.0 N A:GLY143 3.4 35.8 1.0 CA A:GLY143 3.4 35.6 1.0 NAT A:F3F307 3.6 64.5 1.0 O A:THR26 3.7 37.1 1.0 NAQ A:F3F307 4.1 62.2 1.0 C A:GLY143 4.3 31.4 1.0 CAP A:F3F307 4.5 62.8 1.0 C A:ASN142 4.5 36.4 1.0 CB A:LEU27 4.6 33.7 1.0 N A:SER144 4.8 32.3 1.0 CB A:CYS145 4.8 32.5 1.0 C A:THR26 4.8 38.2 1.0 O A:GLY143 4.9 34.0 1.0 N A:CYS145 4.9 33.5 1.0 SG A:CYS145 4.9 40.8 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:58.1 occ:1.00 FAX A:F3F307 0.0 58.1 1.0 CAU A:F3F307 1.3 61.9 1.0 FAW A:F3F307 2.2 55.7 1.0 FAV A:F3F307 2.2 58.7 1.0 CAS A:F3F307 2.3 68.2 1.0 NAT A:F3F307 2.7 64.5 1.0 N A:CYS145 2.8 33.5 1.0 C A:GLY143 2.9 31.4 1.0 CA A:GLY143 2.9 35.6 1.0 N A:SER144 3.1 32.3 1.0 N A:GLY143 3.1 35.8 1.0 CB A:CYS145 3.1 32.5 1.0 CA A:CYS145 3.5 30.8 1.0 NAR A:F3F307 3.5 61.1 1.0 O A:GLY143 3.5 34.0 1.0 SG A:CYS145 3.7 40.8 1.0 C A:SER144 3.8 36.0 1.0 CAP A:F3F307 4.0 62.8 1.0 CA A:SER144 4.0 33.2 1.0 CB A:LEU27 4.1 33.7 1.0 O A:CYS145 4.2 31.4 1.0 NAQ A:F3F307 4.3 62.2 1.0 C A:CYS145 4.4 26.8 1.0 C A:ASN142 4.4 36.4 1.0 O A:THR26 4.5 37.1 1.0 CA A:LEU27 4.7 34.4 1.0 O A:SER144 4.9 30.3 1.0 CD2 A:LEU27 4.9 30.0 1.0 OG A:SER144 5.0 33.2 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:58.7 occ:1.00 FAV A:F3F307 0.0 58.7 1.0 CAU A:F3F307 1.4 61.9 1.0 FAX A:F3F307 2.2 58.1 1.0 FAW A:F3F307 2.2 55.7 1.0 CAS A:F3F307 2.3 68.2 1.0 SG A:CYS145 3.0 40.8 1.0 CB A:CYS145 3.0 32.5 1.0 NAT A:F3F307 3.1 64.5 1.0 NAR A:F3F307 3.3 61.1 1.0 CE1 A:HIS41 3.5 46.6 1.0 CD2 A:LEU27 4.0 30.0 1.0 CAP A:F3F307 4.1 62.8 1.0 N A:CYS145 4.2 33.5 1.0 NAQ A:F3F307 4.2 62.2 1.0 CA A:CYS145 4.2 30.8 1.0 CB A:LEU27 4.3 33.7 1.0 NE2 A:HIS41 4.4 45.4 1.0 ND1 A:HIS41 4.5 42.9 1.0 N A:GLY143 4.7 35.8 1.0 CG A:LEU27 4.7 36.7 1.0 CA A:GLY143 4.9 35.6 1.0 O A:THR26 4.9 37.1 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