Cadmium in PDB 3ao1: Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase, PDB code: 3ao1 was solved by J.Wielens, M.W.Parker, D.K.Chalmers, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.587, 61.997, 81.765, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.8

The binding sites of Cadmium atom in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase (pdb code 3ao1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase, PDB code: 3ao1:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:36.2 occ:1.00 OE2 A:GLU92 1.9 25.7 1.0 NE2 A:HIS67 2.4 31.2 1.0 SG A:CYS65 2.6 29.0 1.0 CD A:GLU92 2.8 35.4 1.0 OE1 A:GLU92 3.0 37.4 1.0 CD2 A:HIS67 3.3 32.9 1.0 CE1 A:HIS67 3.4 33.5 1.0 CB A:CYS65 3.5 33.4 1.0 CD A:CD1004 3.5 36.8 1.0 CG A:GLU92 4.2 33.7 1.0 CG A:HIS67 4.5 32.9 1.0 ND1 A:HIS67 4.5 31.8 1.0 CA A:CYS65 4.8 33.1 1.0 C A:CYS65 5.0 34.3 1.0

Cadmium binding site 2 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1004 b:36.8 occ:1.00 OD2 A:ASP116 2.4 37.3 1.0 OE1 A:GLU92 2.4 37.4 1.0 O A:HOH30 2.5 36.6 1.0 SG A:CYS65 2.6 29.0 1.0 O A:HOH4 2.7 28.0 1.0 CB A:CYS65 3.3 33.4 1.0 CG A:ASP116 3.3 35.1 1.0 CD A:GLU92 3.5 35.4 1.0 CD A:CD1003 3.5 36.2 1.0 OD1 A:ASP116 3.5 35.0 1.0 O A:HOH220 3.8 42.2 1.0 OE2 A:GLU92 4.0 25.7 1.0 N A:CYS65 4.3 34.5 1.0 CA A:CYS65 4.4 33.1 1.0 OD1 A:ASN120 4.7 34.1 1.0 CB A:ASP116 4.7 34.2 1.0 O A:HOH16 4.8 35.2 1.0 CE2 A:PHE121 4.8 35.4 1.0 CG A:GLU92 4.8 33.7 1.0

Cadmium binding site 3 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1001 b:48.2 occ:1.00 OE2 B:GLU92 2.0 44.0 1.0 OD2 B:ASP116 2.2 38.6 1.0 O B:HOH3 2.6 43.9 1.0 SG B:CYS65 2.7 39.2 1.0 O B:HOH213 2.8 33.0 1.0 CD B:GLU92 3.1 47.7 1.0 CG B:ASP116 3.2 45.6 1.0 CB B:CYS65 3.5 44.3 1.0 OD1 B:ASP116 3.5 45.3 1.0 CD B:CD1002 3.5 55.8 1.0 OE1 B:GLU92 3.7 40.9 1.0 CG B:GLU92 4.4 45.2 1.0 N B:CYS65 4.4 40.8 1.0 O B:HOH2 4.5 43.5 1.0 CA B:CYS65 4.6 40.1 1.0 CE2 B:PHE121 4.6 42.8 1.0 CB B:ASP116 4.6 42.6 1.0 OD1 B:ASN120 4.6 46.0 1.0 ND2 B:ASN120 4.8 41.8 1.0

Cadmium binding site 4 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1002 b:55.8 occ:1.00 NE2 B:HIS67 2.2 49.6 1.0 OE1 B:GLU92 2.3 40.9 1.0 SG B:CYS65 2.6 39.2 1.0 O B:HOH224 2.8 40.7 1.0 CD2 B:HIS67 3.1 48.2 1.0 CD B:GLU92 3.2 47.7 1.0 CE1 B:HIS67 3.3 50.5 1.0 OE2 B:GLU92 3.4 44.0 1.0 CD B:CD1001 3.5 48.2 1.0 CB B:CYS65 3.6 44.3 1.0 CG B:HIS67 4.3 49.7 1.0 ND1 B:HIS67 4.3 49.2 1.0 CG B:GLU92 4.6 45.2 1.0 CA B:CYS65 4.9 40.1 1.0

J.Wielens, S.J.Headey, J.J.Deadman, D.I.Rhodes, M.W.Parker, D.K.Chalmers, M.J.Scanlon. Fragment-Based Design of Ligands Targeting A Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus 1 Chemmedchem V. 6 258 2011.
ISSN: ISSN 1860-7179
PubMed: 21275048
DOI: 10.1002/CMDC.201000483