Cadmium in PDB 3vqe: Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol

The structure of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol, PDB code: 3vqe was solved by J.Wielens, D.K.Chalmers, M.W.Parker, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.83 / 1.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	49.460, 49.460, 103.230, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 22.2

The structure of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol (pdb code 3vqe). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol, PDB code: 3vqe:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:20.6 occ:1.00 OE1 A:GLU92 2.2 27.7 1.0 NE2 A:HIS67 2.2 18.0 1.0 SG A:CYS65 2.5 22.3 1.0 CD A:GLU92 2.9 25.7 1.0 OE2 A:GLU92 3.0 23.9 1.0 CE1 A:HIS67 3.1 22.7 1.0 CD2 A:HIS67 3.3 23.2 1.0 CB A:CYS65 3.5 23.6 1.0 CD A:CD1002 3.7 20.9 1.0 ND1 A:HIS67 4.3 27.8 1.0 CG A:GLU92 4.4 22.6 1.0 CG A:HIS67 4.4 22.2 1.0 O A:HOH1137 4.5 33.3 1.0 CA A:CYS65 4.7 18.1 1.0 C A:CYS65 4.8 24.7 1.0 O A:HOH1128 4.9 35.5 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:20.9 occ:1.00 O A:HOH1106 2.3 22.3 1.0 OD2 A:ASP116 2.4 22.9 1.0 CL A:CL1003 2.5 20.1 1.0 OE2 A:GLU92 2.6 23.9 1.0 SG A:CYS65 2.6 22.3 1.0 CG A:ASP116 3.3 19.5 1.0 CD A:GLU92 3.5 25.7 1.0 OD1 A:ASP116 3.6 20.8 1.0 CB A:CYS65 3.6 23.6 1.0 CD A:CD1001 3.7 20.6 1.0 O A:HOH1115 4.0 26.3 1.0 OE1 A:GLU92 4.1 27.7 1.0 OD1 A:ASN120 4.2 22.2 1.0 O A:HOH1109 4.2 21.7 1.0 O A:HOH1113 4.4 21.3 1.0 N A:CYS65 4.5 20.0 1.0 CG A:GLU92 4.5 22.6 1.0 CA A:CYS65 4.6 18.1 1.0 CB A:ASP116 4.7 20.1 1.0 ND2 A:ASN120 4.7 19.9 1.0 CG A:ASN120 4.9 21.4 1.0 CE2 A:PHE121 5.0 19.0 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:20.7 occ:1.00 OE1 B:GLU92 2.2 25.0 1.0 NE2 B:HIS67 2.2 19.1 1.0 SG B:CYS65 2.5 20.9 1.0 CD B:GLU92 2.9 22.9 1.0 OE2 B:GLU92 2.9 23.4 1.0 CE1 B:HIS67 3.1 21.1 1.0 CD2 B:HIS67 3.3 22.2 1.0 CB B:CYS65 3.5 24.4 1.0 CD B:CD302 3.7 20.9 1.0 ND1 B:HIS67 4.3 25.3 1.0 CG B:GLU92 4.4 20.3 1.0 CG B:HIS67 4.4 23.1 1.0 CA B:CYS65 4.7 18.6 1.0 C B:CYS65 4.8 24.1 1.0 O B:HOH424 4.9 34.2 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv-1 in Core Domain in Complex with [1-(4-Fluorophenyl)-5-Methyl-1H- Pyrazol-4-Yl]Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:20.9 occ:1.00 OD2 B:ASP116 2.4 22.4 1.0 O B:HOH403 2.4 21.2 1.0 CL B:CL303 2.5 19.9 1.0 SG B:CYS65 2.6 20.9 1.0 OE2 B:GLU92 2.6 23.4 1.0 CG B:ASP116 3.3 19.5 1.0 CD B:GLU92 3.5 22.9 1.0 OD1 B:ASP116 3.6 21.5 1.0 CB B:CYS65 3.6 24.4 1.0 CD B:CD301 3.7 20.7 1.0 O B:HOH418 4.0 26.7 1.0 OE1 B:GLU92 4.1 25.0 1.0 OD1 B:ASN120 4.2 21.9 1.0 O B:HOH416 4.3 23.5 1.0 N B:CYS65 4.5 20.2 1.0 CG B:GLU92 4.5 20.3 1.0 CA B:CYS65 4.6 18.6 1.0 CB B:ASP116 4.7 20.2 1.0 ND2 B:ASN120 4.7 18.9 1.0 CG B:ASN120 4.9 20.3 1.0

J.Wielens, S.J.Headey, D.I.Rhodes, R.J.Mulder, O.Dolezal, J.J.Deadman, J.Newman, D.K.Chalmers, M.W.Parker, T.S.Peat, M.J.Scanlon. Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification? J Biomol Screen V. 18 147 2013.
ISSN: ISSN 1087-0571
PubMed: 23139382
DOI: 10.1177/1087057112465979