Chlorine in PDB 4dkr: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169, PDB code: 4dkr was solved by Y.D.Kwon, J.M.Lalonde, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, J.Mascola, A.Schon, E.Freire, J.Sodroski, N.Madani, A.B.Smith Iii, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.74 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.443, 68.602, 94.542, 90.00, 91.38, 90.00
R / Rfree (%)	19 / 20.8

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169 (pdb code 4dkr). 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 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169, PDB code: 4dkr:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169


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 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl513 b:40.0 occ:1.00 CL7 A:0LJ513 0.0 40.0 1.0 C02 A:0LJ513 1.7 33.3 1.0 C03 A:0LJ513 2.7 29.4 1.0 C01 A:0LJ513 2.7 35.3 1.0 F08 A:0LJ513 2.9 33.0 1.0 CA A:PHE376 3.5 16.6 1.0 N A:PHE376 3.5 18.1 1.0 C A:PHE376 3.6 23.1 1.0 CD1 A:PHE382 3.8 27.7 1.0 C A:SER375 3.8 24.5 1.0 O A:PHE376 3.9 23.8 1.0 OG A:SER375 3.9 36.3 1.0 C04 A:0LJ513 4.0 23.5 1.0 C06 A:0LJ513 4.0 35.6 1.0 O A:VAL255 4.0 23.0 1.0 O A:SER375 4.0 20.6 1.0 CB A:SER375 4.1 24.7 1.0 N A:ASN377 4.1 21.9 1.0 CE1 A:PHE382 4.1 27.7 1.0 CG1 A:VAL255 4.3 23.5 1.0 C05 A:0LJ513 4.5 31.1 1.0 CA A:SER375 4.6 18.7 1.0 C A:VAL255 4.6 23.7 1.0 CA A:SER256 4.8 20.0 1.0 CB A:ASN377 4.9 23.0 1.0 CA A:ASN377 4.9 21.8 1.0 CB A:PHE376 5.0 21.6 1.0 N A:SER256 5.0 18.4 1.0 CB A:VAL255 5.0 24.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169


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 93TH057 Hiv-1 GP120 Core in Complex with Aws-I-169 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl513 b:52.2 occ:1.00 CL7 C:0LJ513 0.0 52.2 1.0 C02 C:0LJ513 1.7 39.0 1.0 C01 C:0LJ513 2.7 39.1 1.0 C03 C:0LJ513 2.7 39.5 1.0 F08 C:0LJ513 2.9 52.7 1.0 CA C:PHE376 3.6 31.9 1.0 C C:PHE376 3.6 35.1 1.0 O C:VAL255 3.7 33.2 1.0 O C:HOH707 3.9 38.2 1.0 N C:ASN377 3.9 33.1 1.0 N C:PHE376 3.9 26.1 1.0 C06 C:0LJ513 4.0 54.0 1.0 C04 C:0LJ513 4.0 34.0 1.0 O C:PHE376 4.0 30.7 1.0 CD1 C:PHE382 4.1 41.8 1.0 CG1 C:VAL255 4.1 24.0 1.0 C C:SER375 4.3 35.1 1.0 CE1 C:PHE382 4.4 36.5 1.0 O C:SER375 4.4 32.8 1.0 C C:VAL255 4.4 30.7 1.0 CB C:ASN377 4.5 28.1 1.0 CH2 C:TRP112 4.5 26.0 1.0 C05 C:0LJ513 4.5 46.0 1.0 CB C:VAL255 4.6 21.7 1.0 OG C:SER375 4.6 43.5 1.0 CA C:ASN377 4.6 23.8 1.0 CB C:SER375 4.8 38.9 1.0 CB C:PHE376 5.0 27.8 1.0

J.M.Lalonde, Y.D.Kwon, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, A.Schon, E.Freire, P.D.Kwong, J.R.Mascola, J.Sodroski, N.Madani, A.B.Smith. Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule Hiv-1 Entry Inhibitors. J.Med.Chem. V. 55 4382 2012.
ISSN: ISSN 0022-2623
PubMed: 22497421
DOI: 10.1021/JM300265J