Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Clade A/E Hiv-1 GP120 Core in Complex with Nbd- 14010, PDB code: 5u6e:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl512 b:79.3 occ:1.00 CL24 A:82M512 0.0 79.3 1.0 C23 A:82M512 1.8 63.0 1.0 C22 A:82M512 2.7 56.0 1.0 C25 A:82M512 2.8 58.2 1.0 H251 A:82M512 2.9 69.9 1.0 F27 A:82M512 2.9 56.9 1.0 C A:PHE376 3.3 38.7 1.0 O A:PHE376 3.3 34.4 1.0 N A:PHE376 3.3 35.3 1.0 CA A:PHE376 3.4 37.1 1.0 CD2 A:PHE382 3.5 49.0 1.0 C A:SER375 3.7 39.3 1.0 N A:ASN377 3.9 41.6 1.0 C21 A:82M512 4.0 54.7 1.0 C26 A:82M512 4.0 55.3 1.0 CE2 A:PHE382 4.1 48.1 1.0 O A:SER375 4.1 35.5 1.0 CB A:SER375 4.1 45.3 1.0 OG A:SER375 4.2 55.9 1.0 O A:VAL255 4.5 35.9 1.0 CA A:SER375 4.5 39.2 1.0 C20 A:82M512 4.5 53.3 1.0 CA A:ASN377 4.6 43.3 1.0 CG A:PHE382 4.6 46.1 1.0 CB A:ASN377 4.7 41.4 1.0 H211 A:82M512 4.7 65.6 1.0 H261 A:82M512 4.8 66.4 1.0 CB A:PHE382 4.8 39.5 1.0 CB A:PHE376 4.9 37.4 1.0 O A:PHE383 5.0 36.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl508 b:89.0 occ:1.00 CL24 B:82M508 0.0 89.0 1.0 C23 B:82M508 1.8 81.8 1.0 C22 B:82M508 2.7 75.8 1.0 C25 B:82M508 2.8 81.4 1.0 H251 B:82M508 2.9 97.7 1.0 F27 B:82M508 2.9 76.8 1.0 C B:PHE376 3.5 54.5 1.0 CD1 B:PHE382 3.5 57.4 1.0 O B:PHE376 3.6 54.2 1.0 CA B:PHE376 3.6 59.2 1.0 N B:PHE376 3.7 55.8 1.0 N B:ASN377 3.9 54.7 1.0 C21 B:82M508 4.0 74.9 1.0 C26 B:82M508 4.0 79.8 1.0 CE1 B:PHE382 4.2 56.1 1.0 C B:SER375 4.3 58.4 1.0 CB B:ASN377 4.5 48.9 1.0 CA B:ASN377 4.5 52.9 1.0 O B:VAL255 4.5 59.1 1.0 C20 B:82M508 4.5 77.8 1.0 CG B:PHE382 4.6 58.6 1.0 OG B:SER375 4.6 74.7 1.0 CB B:SER375 4.6 70.7 1.0 CB B:PHE382 4.7 59.9 1.0 CH2 B:TRP112 4.7 52.4 1.0 O B:SER375 4.7 57.1 1.0 H211 B:82M508 4.7 89.9 1.0 H261 B:82M508 4.8 95.8 1.0 CA B:PHE382 4.9 57.8 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