Fluorine in PDB 5u6e: Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010

The structure of Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010, PDB code: 5u6e was solved by Y.D.Kwon, A.K.Debnath, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.92 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.181, 68.743, 94.749, 90.00, 91.26, 90.00
R / Rfree (%)	19.3 / 23.1

The structure of Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010 (pdb code 5u6e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010, PDB code: 5u6e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010


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 Hiv-1 GP120 Core in Complex with Nbd- 14010 within 5.0Å range: probe atom residue distance (Å) B Occ A:F512 b:56.9 occ:1.00 F27 A:82M512 0.0 56.9 1.0 C22 A:82M512 1.4 56.0 1.0 C21 A:82M512 2.4 54.7 1.0 C23 A:82M512 2.4 63.0 1.0 H211 A:82M512 2.5 65.6 1.0 CL24 A:82M512 2.9 79.3 1.0 O A:SER375 2.9 35.5 1.0 CA A:SER256 3.0 29.6 1.0 N A:SER256 3.4 29.2 1.0 C A:SER256 3.4 35.5 1.0 OG A:SER375 3.4 55.9 1.0 O A:VAL255 3.5 35.9 1.0 C A:SER375 3.5 39.3 1.0 C A:VAL255 3.6 33.5 1.0 C20 A:82M512 3.6 53.3 1.0 N A:THR257 3.6 32.3 1.0 C25 A:82M512 3.6 58.2 1.0 CG1 A:VAL255 3.7 36.5 1.0 N A:PHE376 4.0 35.3 1.0 CG2 A:THR257 4.0 35.3 1.0 CA A:PHE376 4.1 37.1 1.0 O A:SER256 4.1 35.6 1.0 C26 A:82M512 4.1 55.3 1.0 CB A:SER375 4.2 45.3 1.0 CB A:SER256 4.4 32.0 1.0 H251 A:82M512 4.4 69.9 1.0 CA A:SER375 4.5 39.2 1.0 CB A:VAL255 4.5 37.5 1.0 CA A:VAL255 4.6 33.1 1.0 H171 A:82M512 4.8 57.4 1.0 CA A:THR257 4.8 29.8 1.0 CB A:THR257 4.8 37.0 1.0 CD1 A:ILE475 4.8 41.9 1.0 C18 A:82M512 4.9 51.7 1.0 OG1 A:THR257 4.9 38.9 1.0 C A:PHE376 4.9 38.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010


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 Hiv-1 GP120 Core in Complex with Nbd- 14010 within 5.0Å range: probe atom residue distance (Å) B Occ B:F508 b:76.8 occ:1.00 F27 B:82M508 0.0 76.8 1.0 C22 B:82M508 1.4 75.8 1.0 C23 B:82M508 2.4 81.8 1.0 C21 B:82M508 2.4 74.9 1.0 H211 B:82M508 2.6 89.9 1.0 CL24 B:82M508 2.9 89.0 1.0 O B:VAL255 3.3 59.1 1.0 O B:SER375 3.3 57.1 1.0 CA B:SER256 3.5 52.2 1.0 OG B:SER375 3.5 74.7 1.0 CG1 B:VAL255 3.6 50.7 1.0 C B:VAL255 3.6 51.1 1.0 C20 B:82M508 3.6 77.8 1.0 C25 B:82M508 3.6 81.4 1.0 N B:SER256 3.7 50.2 1.0 C B:SER375 3.7 58.4 1.0 C B:SER256 3.8 52.4 1.0 N B:PHE376 4.0 55.8 1.0 CA B:PHE376 4.0 59.2 1.0 N B:THR257 4.1 54.0 1.0 C26 B:82M508 4.1 79.8 1.0 CB B:SER375 4.3 70.7 1.0 CG2 B:THR257 4.3 54.6 1.0 CB B:VAL255 4.4 46.4 1.0 H251 B:82M508 4.4 97.7 1.0 O B:SER256 4.4 53.3 1.0 CA B:VAL255 4.6 47.1 1.0 CA B:SER375 4.7 62.8 1.0 C B:PHE376 4.8 54.5 1.0 CB B:SER256 4.9 50.7 1.0 H171 B:82M508 4.9 96.7 1.0 C18 B:82M508 4.9 80.8 1.0

F.Curreli, Y.D.Kwon, D.S.Belov, R.R.Ramesh, A.V.Kurkin, A.Altieri, P.D.Kwong, A.K.Debnath. Synthesis, Antiviral Potency, in Vitro Admet, and X-Ray Structure of Potent CD4 Mimics As Entry Inhibitors That Target the PHE43 Cavity of Hiv-1 GP120. J. Med. Chem. V. 60 3124 2017.
ISSN: ISSN 1520-4804
PubMed: 28266845
DOI: 10.1021/ACS.JMEDCHEM.7B00179