Chlorine in PDB 4rz8: Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist

The structure of Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist, PDB code: 4rz8 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)	44.03 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	113.621, 68.842, 116.192, 90.00, 110.59, 90.00
R / Rfree (%)	22.7 / 24.4

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist (pdb code 4rz8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist, PDB code: 4rz8:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist


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 Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl510 b:0.2 occ:1.00 CL21 A:3ZM510 0.0 0.2 1.0 C18 A:3ZM510 1.8 63.3 1.0 C19 A:3ZM510 2.8 63.7 1.0 C17 A:3ZM510 2.8 61.3 1.0 H191 A:3ZM510 2.9 76.4 1.0 H171 A:3ZM510 2.9 73.5 1.0 C A:PHE376 3.3 48.5 1.0 CD1 A:PHE382 3.3 51.4 1.0 N A:ASN377 3.4 47.8 1.0 CA A:PHE376 3.5 50.7 1.0 O A:PHE376 3.7 47.3 1.0 CE1 A:PHE382 3.7 48.7 1.0 N A:PHE376 3.8 46.1 1.0 CB A:ASN377 4.0 45.1 1.0 C20 A:3ZM510 4.1 63.8 1.0 CA A:ASN377 4.1 46.3 1.0 C16 A:3ZM510 4.1 62.3 1.0 O A:VAL255 4.1 48.0 1.0 CH2 A:TRP112 4.2 43.6 1.0 C A:SER375 4.4 48.0 1.0 CG A:PHE382 4.5 46.3 1.0 O A:SER375 4.7 48.2 1.0 C15 A:3ZM510 4.7 63.0 1.0 CG1 A:VAL255 4.7 42.8 1.0 CB A:PHE382 4.8 46.1 1.0 CZ3 A:TRP112 4.9 40.0 1.0 H161 A:3ZM510 4.9 74.8 1.0 H201 A:3ZM510 4.9 76.6 1.0 ND2 A:ASN377 4.9 46.1 1.0 CB A:PHE376 4.9 50.1 1.0 C A:VAL255 5.0 47.7 1.0 O A:HOH628 5.0 49.1 1.0 CB A:SER375 5.0 60.3 1.0 CA A:PHE382 5.0 45.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist


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 Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl510 b:88.9 occ:1.00 CL21 B:3ZM510 0.0 88.9 1.0 C18 B:3ZM510 1.8 50.7 1.0 C19 B:3ZM510 2.8 51.4 1.0 C17 B:3ZM510 2.8 46.6 1.0 H191 B:3ZM510 2.9 61.7 1.0 H171 B:3ZM510 2.9 55.9 1.0 C B:PHE376 3.2 43.6 1.0 CA B:PHE376 3.4 40.7 1.0 N B:ASN377 3.4 38.2 1.0 CD2 B:PHE382 3.7 46.3 1.0 O B:PHE376 3.7 43.9 1.0 N B:PHE376 3.7 42.0 1.0 O B:VAL255 3.8 40.1 1.0 CE2 B:PHE382 4.1 41.6 1.0 CB B:ASN377 4.1 41.8 1.0 C20 B:3ZM510 4.1 49.6 1.0 C16 B:3ZM510 4.1 48.5 1.0 CA B:ASN377 4.2 41.7 1.0 C B:SER375 4.3 44.4 1.0 CH2 B:TRP112 4.3 39.2 1.0 O B:SER375 4.4 40.7 1.0 CG1 B:VAL255 4.5 39.7 1.0 C B:VAL255 4.6 39.5 1.0 C15 B:3ZM510 4.7 49.3 1.0 CB B:PHE376 4.8 40.8 1.0 CG B:PHE382 4.8 45.0 1.0 CB B:VAL255 4.9 36.3 1.0 H201 B:3ZM510 4.9 59.6 1.0 H161 B:3ZM510 4.9 58.2 1.0 CB B:SER375 4.9 52.1 1.0 OG B:SER375 5.0 57.6 1.0 CZ3 B:TRP112 5.0 39.8 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl512 b:83.6 occ:1.00 CL21 C:3ZM512 0.0 83.6 1.0 C18 C:3ZM512 1.8 44.4 1.0 C19 C:3ZM512 2.8 48.6 1.0 C17 C:3ZM512 2.8 43.8 1.0 H191 C:3ZM512 2.9 58.4 1.0 H171 C:3ZM512 2.9 52.5 1.0 C C:PHE376 3.1 33.0 1.0 N C:ASN377 3.2 32.4 1.0 CA C:PHE376 3.4 29.0 1.0 CD1 C:PHE382 3.6 41.6 1.0 O C:PHE376 3.6 31.3 1.0 N C:PHE376 3.8 28.7 1.0 CB C:ASN377 3.8 36.1 1.0 CA C:ASN377 3.9 34.0 1.0 CE1 C:PHE382 3.9 39.5 1.0 O C:VAL255 3.9 30.3 1.0 C20 C:3ZM512 4.1 47.3 1.0 C16 C:3ZM512 4.1 43.4 1.0 C C:SER375 4.3 31.2 1.0 CH2 C:TRP112 4.4 42.0 1.0 O C:SER375 4.5 31.1 1.0 CG1 C:VAL255 4.6 30.0 1.0 C15 C:3ZM512 4.7 46.2 1.0 CG C:PHE382 4.7 39.1 1.0 C C:VAL255 4.7 28.1 1.0 O C:HOH607 4.8 38.1 1.0 CB C:PHE376 4.8 30.5 1.0 ND2 C:ASN377 4.8 40.7 1.0 CG C:ASN377 4.9 41.4 1.0 CB C:VAL255 4.9 29.6 1.0 H201 C:3ZM512 4.9 56.7 1.0 H161 C:3ZM512 4.9 52.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hiv-1 GP120 Core in Complex with Nbd-11021, A Small Molecule CD4-Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl512 b:99.2 occ:1.00 CL21 D:3ZM512 0.0 99.2 1.0 C18 D:3ZM512 1.8 52.0 1.0 C19 D:3ZM512 2.8 55.3 1.0 C17 D:3ZM512 2.8 50.3 1.0 H191 D:3ZM512 2.9 66.4 1.0 H171 D:3ZM512 2.9 60.3 1.0 C D:PHE376 3.1 34.0 1.0 CA D:PHE376 3.2 30.9 1.0 N D:PHE376 3.4 29.1 1.0 N D:ASN377 3.5 34.4 1.0 CD1 D:PHE382 3.5 39.5 1.0 O D:PHE376 3.5 30.3 1.0 C D:SER375 3.8 34.8 1.0 CE1 D:PHE382 4.0 38.1 1.0 C20 D:3ZM512 4.1 54.9 1.0 O D:SER375 4.1 32.2 1.0 C16 D:3ZM512 4.1 50.8 1.0 O D:VAL255 4.2 26.6 1.0 CA D:ASN377 4.2 35.5 1.0 CB D:ASN377 4.3 36.0 1.0 CB D:SER375 4.4 41.8 1.0 OG D:SER375 4.6 50.7 1.0 CG D:PHE382 4.6 37.7 1.0 C15 D:3ZM512 4.7 52.2 1.0 CA D:SER375 4.7 33.9 1.0 CB D:PHE376 4.7 32.7 1.0 CG1 D:VAL255 4.8 25.1 1.0 C D:VAL255 4.9 26.5 1.0 H201 D:3ZM512 4.9 65.9 1.0 H161 D:3ZM512 4.9 60.9 1.0 CB D:PHE382 4.9 34.5 1.0

F.Curreli, Y.D.Kwon, H.Zhang, D.Scacalossi, D.S.Belov, A.A.Tikhonov, I.A.Andreev, A.Altieri, A.V.Kurkin, P.D.Kwong, A.K.Debnath. Structure-Based Design of A Small Molecule CD4-Antagonist with Broad Spectrum Anti-Hiv-1 Activity. J.Med.Chem. V. 58 6909 2015.
ISSN: ISSN 0022-2623
PubMed: 26301736
DOI: 10.1021/ACS.JMEDCHEM.5B00709