Fluorine in PDB 6sk5: Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340

All present enzymatic activity of Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340:
2.7.7.48; 3.4.22.28; 3.4.22.29; 3.6.1.15;

The binding sites of Fluorine atom in the Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340 (pdb code 6sk5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340, PDB code: 6sk5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:37.5 occ:1.00 F1 A:LGQ301 0.0 37.5 1.0 C18 A:LGQ301 1.4 35.5 1.0 F3 A:LGQ301 2.2 36.0 1.0 F2 A:LGQ301 2.2 37.1 1.0 C5 A:LGQ301 2.3 29.3 1.0 C3 A:LGQ301 2.7 33.5 1.0 HE1 A:PHE124 3.2 20.6 1.0 HD11 A:LEU106 3.4 26.0 1.0 HG A:SER126 3.4 24.4 1.0 C6 A:LGQ301 3.5 33.5 1.0 OG A:SER126 3.6 24.4 1.0 HE2 A:MET221 3.6 25.5 1.0 HH A:TYR197 4.0 24.9 1.0 C1 A:LGQ301 4.0 35.6 1.0 CE1 A:PHE124 4.0 20.6 1.0 HZ A:PHE124 4.1 16.8 1.0 OH A:TYR197 4.1 24.9 1.0 HG A:LEU106 4.2 24.3 1.0 NE2 A:HIS245 4.2 20.4 1.0 HD21 A:LEU106 4.2 25.9 1.0 CD1 A:LEU106 4.2 26.0 1.0 OH A:TYR128 4.3 24.6 1.0 CZ A:TYR197 4.3 19.6 1.0 HE2 A:TYR197 4.4 18.7 1.0 HD12 A:LEU106 4.4 26.0 1.0 HH A:TYR128 4.4 24.6 1.0 CZ A:PHE124 4.4 16.8 1.0 CE A:MET221 4.5 25.5 1.0 CE2 A:TYR197 4.5 18.7 1.0 HE1 A:MET221 4.5 25.5 1.0 CG A:LEU106 4.6 24.3 1.0 C4 A:LGQ301 4.6 35.2 1.0 HG21 A:ILE104 4.8 26.0 1.0 CB A:SER126 4.8 21.4 1.0 HD2 A:HIS245 4.8 20.7 1.0 CD2 A:HIS245 4.8 20.7 1.0 C2 A:LGQ301 4.8 34.2 1.0 CD2 A:LEU106 4.9 25.9 1.0 HB2 A:SER126 4.9 21.4 1.0 HB3 A:SER126 4.9 21.4 1.0 CE1 A:HIS245 5.0 22.2 1.0 HG22 A:ILE104 5.0 26.0 1.0 HD13 A:LEU106 5.0 26.0 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:37.1 occ:1.00 F2 A:LGQ301 0.0 37.1 1.0 C18 A:LGQ301 1.4 35.5 1.0 HE2 A:MET221 2.0 25.5 1.0 F3 A:LGQ301 2.2 36.0 1.0 F1 A:LGQ301 2.2 37.5 1.0 C5 A:LGQ301 2.3 29.3 1.0 HG21 A:ILE104 2.7 26.0 1.0 CE A:MET221 2.9 25.5 1.0 C6 A:LGQ301 3.1 33.5 1.0 C3 A:LGQ301 3.2 33.5 1.0 HE1 A:MET221 3.2 25.5 1.0 HE3 A:MET221 3.2 25.5 1.0 HG22 A:ILE104 3.4 26.0 1.0 CG2 A:ILE104 3.4 26.0 1.0 HH A:TYR128 3.4 24.6 1.0 OH A:TYR128 3.4 24.6 1.0 HG23 A:ILE104 3.6 26.0 1.0 HG3 A:MET221 3.7 31.3 1.0 HB3 A:MET221 4.1 28.2 1.0 SD A:MET221 4.2 33.4 1.0 C4 A:LGQ301 4.3 35.2 1.0 CG A:MET221 4.3 31.3 1.0 C1 A:LGQ301 4.4 35.6 1.0 HD12 A:LEU191 4.6 23.1 1.0 CB A:ILE104 4.7 22.6 1.0 CB A:MET221 4.8 28.2 1.0 OH A:TYR197 4.8 24.9 1.0 CZ A:TYR128 4.8 19.1 1.0 C2 A:LGQ301 4.8 34.2 1.0 HG13 A:ILE104 4.9 24.0 1.0 HB A:ILE104 4.9 22.6 1.0 HG A:LEU106 4.9 24.3 1.0 HH A:TYR197 4.9 24.9 1.0 HD12 A:ILE104 4.9 27.1 1.0 HG A:SER126 4.9 24.4 1.0 OG A:SER126 5.0 24.4 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Rhinovirus-B5 Complexed to Antiviral Obr-5-340 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:36.0 occ:1.00 F3 A:LGQ301 0.0 36.0 1.0 C18 A:LGQ301 1.3 35.5 1.0 F1 A:LGQ301 2.2 37.5 1.0 F2 A:LGQ301 2.2 37.1 1.0 C5 A:LGQ301 2.3 29.3 1.0 C6 A:LGQ301 2.7 33.5 1.0 HD21 A:LEU106 2.8 25.9 1.0 HG A:LEU106 3.0 24.3 1.0 HH A:TYR128 3.1 24.6 1.0 HD11 A:LEU106 3.3 26.0 1.0 HG23 A:ILE104 3.4 26.0 1.0 OH A:TYR128 3.4 24.6 1.0 HG22 A:ILE104 3.5 26.0 1.0 C3 A:LGQ301 3.5 33.5 1.0 CD2 A:LEU106 3.5 25.9 1.0 HG21 A:ILE104 3.5 26.0 1.0 CG A:LEU106 3.6 24.3 1.0 CG2 A:ILE104 3.7 26.0 1.0 HD23 A:LEU106 3.7 25.9 1.0 CD1 A:LEU106 3.9 26.0 1.0 C4 A:LGQ301 4.0 35.2 1.0 HE2 A:MET221 4.0 25.5 1.0 HD2 A:HIS245 4.2 20.7 1.0 HD22 A:LEU106 4.3 25.9 1.0 NE2 A:HIS245 4.4 20.4 1.0 HD12 A:LEU106 4.4 26.0 1.0 CD2 A:HIS245 4.4 20.7 1.0 HG A:SER126 4.4 24.4 1.0 CZ A:TYR128 4.5 19.1 1.0 C1 A:LGQ301 4.6 35.6 1.0 HD13 A:LEU106 4.7 26.0 1.0 O A:ASN105 4.8 28.7 1.0 C A:ASN105 4.8 27.8 1.0 HE2 A:TYR128 4.8 18.1 1.0 C2 A:LGQ301 4.8 34.2 1.0 OG A:SER126 4.8 24.4 1.0 HG3 A:MET221 4.8 31.3 1.0 HE1 A:PHE124 4.8 20.6 1.0 HA A:ASN105 4.8 25.9 1.0 HD12 A:ILE104 4.9 27.1 1.0 CB A:LEU106 5.0 23.1 1.0 H A:ASN105 5.0 27.1 1.0 CE A:MET221 5.0 25.5 1.0

J.Wald, M.Pasin, M.Richter, C.Walther, N.Mathai, J.Kirchmair, V.A.Makarov, N.Goessweiner-Mohr, T.C.Marlovits, I.Zanella, A.Real-Hohn, N.Verdaguer, D.Blaas, M.Schmidtke. Cryo-Em Structure of Pleconaril-Resistant Rhinovirus-B5 Complexed to the Antiviral Obr-5-340 Reveals Unexpected Binding Site. Proc.Natl.Acad.Sci.Usa V. 116 19109 2019.
ISSN: ESSN 1091-6490
PubMed: 31462495
DOI: 10.1073/PNAS.1904732116