Fluorine in PDB 8f9z: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist, PDB code: 8f9z was solved by Y.D.Kwon, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.44 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.196, 67.592, 87.907, 90, 90, 90
R / Rfree (%)	18.3 / 21.6

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist (pdb code 8f9z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist, PDB code: 8f9z:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist


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 Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:41.2 occ:1.00 F19 A:XKW507 0.0 41.2 1.0 C18 A:XKW507 1.3 45.4 1.0 F21 A:XKW507 2.1 36.6 1.0 F20 A:XKW507 2.1 48.8 1.0 C15 A:XKW507 2.4 29.9 1.0 HH2 A:TRP112 2.9 12.7 1.0 HE2 A:PHE382 3.0 25.3 1.0 H161 A:XKW507 3.0 49.8 1.0 C16 A:XKW507 3.1 41.4 1.0 HD2 A:PHE382 3.2 23.8 1.0 HG12 A:VAL255 3.3 13.4 1.0 HD1 A:TRP427 3.5 15.6 1.0 C14 A:XKW507 3.5 24.9 1.0 CH2 A:TRP112 3.6 10.5 1.0 H141 A:XKW507 3.6 29.9 1.0 CE2 A:PHE382 3.6 21.0 1.0 HB2 A:ASN377 3.8 18.4 1.0 CD2 A:PHE382 3.8 19.7 1.0 O A:HOH720 3.8 25.6 1.0 O A:HOH662 3.9 30.1 1.0 HB A:VAL255 3.9 8.7 1.0 HG11 A:VAL255 3.9 13.4 1.0 HZ3 A:TRP112 3.9 13.9 1.0 CG1 A:VAL255 4.0 11.1 1.0 CZ3 A:TRP112 4.1 11.5 1.0 CD1 A:TRP427 4.1 12.9 1.0 HA A:PHE376 4.2 17.1 1.0 O A:HOH705 4.3 29.5 1.0 N17 A:XKW507 4.4 47.3 1.0 O A:VAL255 4.4 11.8 1.0 CZ2 A:TRP112 4.4 10.0 1.0 CB A:VAL255 4.5 7.2 1.0 HZ2 A:TRP112 4.5 12.1 1.0 C A:PHE376 4.6 18.6 1.0 HE1 A:TRP427 4.6 17.3 1.0 N A:ASN377 4.7 18.3 1.0 C13 A:XKW507 4.7 38.4 1.0 HB3 A:TRP427 4.7 18.2 1.0 CB A:ASN377 4.7 15.2 1.0 HD22 A:ASN377 4.7 24.1 1.0 NE1 A:TRP427 4.7 14.4 1.0 H A:ASN377 4.7 22.0 1.0 CA A:PHE376 4.8 14.2 1.0 HG13 A:VAL255 4.8 13.4 1.0 O A:PHE376 4.9 12.3 1.0 CZ A:PHE382 4.9 20.9 1.0 C A:VAL255 4.9 10.1 1.0 HB2 A:SER375 5.0 16.1 1.0 HB3 A:ASN377 5.0 18.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist


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 Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:48.8 occ:1.00 F20 A:XKW507 0.0 48.8 1.0 C18 A:XKW507 1.3 45.4 1.0 F19 A:XKW507 2.1 41.2 1.0 F21 A:XKW507 2.1 36.6 1.0 O A:HOH705 2.3 29.5 1.0 O A:HOH662 2.4 30.1 1.0 C15 A:XKW507 2.4 29.9 1.0 HD2 A:PHE382 2.5 23.8 1.0 H161 A:XKW507 2.9 49.8 1.0 C16 A:XKW507 3.0 41.4 1.0 HB2 A:SER375 3.0 16.1 1.0 CD2 A:PHE382 3.4 19.7 1.0 C14 A:XKW507 3.5 24.9 1.0 O A:PHE376 3.7 12.3 1.0 H141 A:XKW507 3.7 29.9 1.0 N A:PHE376 3.7 9.6 1.0 HA A:PHE376 3.7 17.1 1.0 HE2 A:PHE382 3.8 25.3 1.0 H A:PHE376 3.8 11.7 1.0 C A:PHE376 3.8 18.6 1.0 CB A:SER375 3.8 13.4 1.0 OG A:SER375 3.9 18.7 1.0 HB3 A:PHE382 4.0 17.6 1.0 CA A:PHE376 4.0 14.2 1.0 C A:SER375 4.0 12.6 1.0 CE2 A:PHE382 4.0 21.0 1.0 N17 A:XKW507 4.3 47.3 1.0 HB2 A:ASN377 4.3 18.4 1.0 HA A:PHE382 4.3 12.1 1.0 CG A:PHE382 4.5 12.1 1.0 N A:ASN377 4.5 18.3 1.0 CA A:SER375 4.5 10.4 1.0 O A:SER375 4.5 13.2 1.0 HB3 A:SER375 4.6 16.1 1.0 CB A:PHE382 4.6 14.6 1.0 HH2 A:TRP112 4.6 12.7 1.0 C13 A:XKW507 4.7 38.4 1.0 HA A:SER375 4.7 12.6 1.0 HG A:SER375 4.7 22.5 1.0 O A:PHE383 4.8 9.0 1.0 HG12 A:VAL255 4.8 13.4 1.0 HG3 A:GLU370 4.8 28.6 1.0 H A:ASN377 4.9 22.0 1.0 H A:PHE383 4.9 10.1 1.0 HE1 A:TYR384 4.9 18.3 1.0 HA A:ASN377 4.9 16.8 1.0 O A:HOH720 4.9 25.6 1.0 CA A:PHE382 4.9 10.0 1.0 OH A:TYR384 5.0 18.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14204, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:36.6 occ:1.00 F21 A:XKW507 0.0 36.6 1.0 C18 A:XKW507 1.3 45.4 1.0 F19 A:XKW507 2.1 41.2 1.0 F20 A:XKW507 2.1 48.8 1.0 C15 A:XKW507 2.4 29.9 1.0 H141 A:XKW507 2.5 29.9 1.0 HA A:PHE376 2.5 17.1 1.0 C14 A:XKW507 2.8 24.9 1.0 HA A:SER256 3.1 8.7 1.0 HG12 A:VAL255 3.2 13.4 1.0 CA A:PHE376 3.2 14.2 1.0 O A:VAL255 3.2 11.8 1.0 O A:SER375 3.3 13.2 1.0 N A:PHE376 3.4 9.6 1.0 C A:SER375 3.4 12.6 1.0 C16 A:XKW507 3.7 41.4 1.0 OG A:SER375 3.7 18.7 1.0 C A:PHE376 3.7 18.6 1.0 HB2 A:SER375 3.8 16.1 1.0 C A:VAL255 3.9 10.1 1.0 O A:HOH720 3.9 25.6 1.0 H A:PHE376 3.9 11.7 1.0 O A:HOH705 4.0 29.5 1.0 H161 A:XKW507 4.0 49.8 1.0 CA A:SER256 4.0 7.1 1.0 CG1 A:VAL255 4.1 11.1 1.0 CB A:SER375 4.1 13.4 1.0 HB A:VAL255 4.2 8.7 1.0 N A:ASN377 4.2 18.3 1.0 C13 A:XKW507 4.2 38.4 1.0 H A:ASN377 4.2 22.0 1.0 O A:PHE376 4.2 12.3 1.0 HG A:SER375 4.3 22.5 1.0 N A:SER256 4.3 9.7 1.0 O A:HOH662 4.4 30.1 1.0 HD2 A:PHE382 4.4 23.8 1.0 CA A:SER375 4.4 10.4 1.0 HG11 A:VAL255 4.5 13.4 1.0 HG23 A:THR257 4.5 20.3 1.0 HB2 A:ASN377 4.5 18.4 1.0 CB A:VAL255 4.6 7.2 1.0 CB A:PHE376 4.6 14.0 1.0 HH2 A:TRP112 4.6 12.7 1.0 HB3 A:PHE376 4.7 16.9 1.0 H A:THR257 4.7 9.3 1.0 HG13 A:VAL255 4.7 13.4 1.0 H131 A:XKW507 4.7 46.2 1.0 O A:HOH681 4.8 17.8 1.0 C A:SER256 4.8 14.3 1.0 N17 A:XKW507 4.8 47.3 1.0 HB2 A:PHE376 4.9 16.9 1.0 CA A:VAL255 4.9 8.9 1.0 HA A:SER375 4.9 12.6 1.0 HE2 A:PHE382 4.9 25.3 1.0 HB3 A:SER256 4.9 13.9 1.0 H A:SER256 5.0 11.8 1.0

F.Curreli, Y.D.Kwon, I.Nicolau, G.Burgos, A.Altieri, A.V.Kurkin, R.Verardi, P.D.Kwong, A.K.Debnath. Antiviral Activity and Crystal Structures of Hiv-1 GP120 Antagonists. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36555641
DOI: 10.3390/IJMS232415999