Cadmium in PDB 3ao4: Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase, PDB code: 3ao4 was solved by J.Wielens, S.J.Headey, 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)	38.72 / 1.95
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	48.200, 48.200, 103.600, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 25.3

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase (pdb code 3ao4). 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 on Hiv-1 Integrase, PDB code: 3ao4:
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 on 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 on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:31.0 occ:1.00 OE1 A:GLU92 1.6 22.1 1.0 NE2 A:HIS67 2.4 34.5 1.0 SG A:CYS65 2.4 27.7 1.0 CD A:GLU92 2.6 30.5 1.0 OE2 A:GLU92 2.8 34.4 1.0 CB A:CYS65 3.2 28.1 1.0 CD2 A:HIS67 3.3 31.7 1.0 CE1 A:HIS67 3.4 37.2 1.0 CD A:CD1002 3.6 32.6 1.0 O A:HOH6 3.7 26.4 1.0 CG A:GLU92 4.1 30.9 1.0 CG A:HIS67 4.5 36.5 1.0 ND1 A:HIS67 4.5 35.5 1.0 CA A:CYS65 4.6 24.1 1.0 C A:CYS65 4.8 27.9 1.0 CB A:GLU92 4.8 31.9 1.0 CG1 A:VAL72 4.9 28.0 1.0

Cadmium binding site 2 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:32.6 occ:1.00 OD2 A:ASP116 2.3 30.6 1.0 OE2 A:GLU92 2.3 34.4 1.0 O A:HOH19 2.4 29.1 1.0 O A:HOH6 2.4 26.4 1.0 CL A:CL501 2.5 30.7 1.0 SG A:CYS65 2.6 27.7 1.0 CD A:GLU92 3.3 30.5 1.0 CG A:ASP116 3.3 33.3 1.0 CB A:CYS65 3.5 28.1 1.0 OD1 A:ASP116 3.6 34.4 1.0 CD A:CD1001 3.6 31.0 1.0 OE1 A:GLU92 3.8 22.1 1.0 OD1 A:ASN120 4.2 29.2 1.0 CG A:GLU92 4.3 30.9 1.0 O A:HOH18 4.3 29.1 1.0 N A:CYS65 4.4 27.0 1.0 O A:HOH8 4.5 31.4 1.0 ND2 A:ASN120 4.6 30.3 1.0 CA A:CYS65 4.6 24.1 1.0 CB A:ASP116 4.7 33.2 1.0 CG A:ASN120 4.8 27.1 1.0

Cadmium binding site 3 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1003 b:30.8 occ:1.00 OE1 B:GLU92 1.6 25.6 1.0 NE2 B:HIS67 2.3 37.1 1.0 SG B:CYS65 2.4 29.2 1.0 CD B:GLU92 2.6 30.6 1.0 OE2 B:GLU92 2.8 35.9 1.0 CB B:CYS65 3.2 27.8 1.0 CE1 B:HIS67 3.2 36.7 1.0 CD2 B:HIS67 3.3 37.8 1.0 O B:HOH31 3.6 28.9 1.0 CD B:CD1004 3.6 32.2 1.0 CG B:GLU92 4.1 31.5 1.0 ND1 B:HIS67 4.3 36.4 1.0 CG B:HIS67 4.4 38.2 1.0 CA B:CYS65 4.5 25.4 1.0 C B:CYS65 4.8 28.6 1.0 CB B:GLU92 4.9 30.6 1.0 CG2 B:VAL72 4.9 27.0 1.0

Cadmium binding site 4 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1004 b:32.2 occ:1.00 OE2 B:GLU92 2.3 35.9 1.0 OD2 B:ASP116 2.3 34.7 1.0 O B:HOH31 2.4 28.9 1.0 O B:HOH45 2.4 28.3 1.0 CL B:CL502 2.5 29.9 1.0 SG B:CYS65 2.6 29.2 1.0 CD B:GLU92 3.3 30.6 1.0 CG B:ASP116 3.4 33.6 1.0 CB B:CYS65 3.5 27.8 1.0 OD1 B:ASP116 3.6 34.5 1.0 CD B:CD1003 3.6 30.8 1.0 O B:HOH16 3.9 24.6 1.0 OE1 B:GLU92 3.9 25.6 1.0 OD1 B:ASN120 4.1 27.2 1.0 O B:HOH10 4.2 27.7 1.0 CG B:GLU92 4.3 31.5 1.0 N B:CYS65 4.4 26.4 1.0 ND2 B:ASN120 4.5 25.6 1.0 CA B:CYS65 4.6 25.4 1.0 O B:HOH20 4.6 32.4 1.0 CG B:ASN120 4.7 25.9 1.0 CB B:ASP116 4.7 32.6 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