Cadmium in PDB 3vq6: Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol

The structure of Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol, PDB code: 3vq6 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)	49.33 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.452, 61.928, 81.674, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.6

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol (pdb code 3vq6). 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-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol, PDB code: 3vq6:
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-Methyl-5-Phenyl-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-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:28.1 occ:0.70 OE1 A:GLU92 1.8 17.3 1.0 O A:HOH432 1.9 29.6 1.0 NE2 A:HIS67 2.4 31.0 1.0 SG A:CYS65 2.4 33.1 1.0 CD A:GLU92 2.6 36.7 1.0 OE2 A:GLU92 2.7 43.5 1.0 CD2 A:HIS67 3.2 29.1 1.0 CB A:CYS65 3.4 31.1 1.0 O A:HOH424 3.5 43.7 1.0 CD A:CD302 3.5 35.4 1.0 CE1 A:HIS67 3.5 28.4 1.0 CG A:GLU92 4.0 37.0 1.0 CG A:HIS67 4.5 28.1 1.0 ND1 A:HIS67 4.6 32.1 1.0 CA A:CYS65 4.7 30.0 1.0 C A:CYS65 4.8 35.1 1.0

Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-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-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:35.4 occ:1.00 O A:HOH421 2.3 41.4 1.0 OE2 A:GLU92 2.3 43.5 1.0 OD2 A:ASP116 2.4 35.3 1.0 SG A:CYS65 2.5 33.1 1.0 O A:HOH406 2.8 33.0 1.0 CB A:CYS65 3.2 31.1 1.0 CG A:ASP116 3.3 34.0 1.0 OD1 A:ASP116 3.4 32.3 1.0 CD A:CD301 3.5 28.1 0.7 CD A:GLU92 3.5 36.7 1.0 O A:HOH424 3.7 43.7 1.0 OE1 A:GLU92 4.0 17.3 1.0 OD1 A:ASP64 4.2 55.9 1.0 N A:CYS65 4.4 37.3 1.0 O A:HOH432 4.4 29.6 1.0 CA A:CYS65 4.4 30.0 1.0 OD1 A:ASN120 4.5 32.6 1.0 CG A:GLU92 4.6 37.0 1.0 CB A:ASP116 4.7 25.6 1.0 CE2 A:PHE121 4.8 33.1 1.0 C A:ASP64 4.9 41.1 1.0 ND2 A:ASN120 5.0 30.1 1.0

Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-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-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:49.0 occ:1.00 OD1 B:ASP116 1.9 37.7 1.0 OE2 B:GLU92 2.1 43.1 1.0 SG B:CYS65 2.6 42.2 1.0 O B:HOH406 2.8 46.5 1.0 O B:HOH404 3.0 35.5 1.0 CG B:ASP116 3.1 54.7 1.0 CD B:GLU92 3.2 43.0 1.0 CB B:CYS65 3.3 45.1 1.0 OD2 B:ASP116 3.5 58.4 1.0 OE1 B:GLU92 3.6 38.0 1.0 CD B:CD302 3.6 56.6 1.0 CE2 B:PHE121 4.2 46.0 1.0 N B:CYS65 4.2 46.6 1.0 OD1 B:ASN120 4.3 44.8 1.0 CA B:CYS65 4.4 40.0 1.0 CB B:ASP116 4.4 49.0 1.0 CG B:GLU92 4.5 43.7 1.0 O B:HOH430 4.8 54.4 1.0 O B:HOH409 4.8 35.8 1.0 ND2 B:ASN120 4.8 41.9 1.0 CG B:ASN120 4.9 48.9 1.0

Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with (1-Methyl-5-Phenyl-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-Methyl-5-Phenyl-1H-Pyrazol-4- Yl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:56.6 occ:1.00 OE1 B:GLU92 2.3 38.0 1.0 NE2 B:HIS67 2.3 57.9 1.0 O B:HOH409 2.6 35.8 1.0 SG B:CYS65 2.7 42.2 1.0 CE1 B:HIS67 3.2 57.3 1.0 CD B:GLU92 3.3 43.0 1.0 CD2 B:HIS67 3.4 57.1 1.0 O B:HOH406 3.5 46.5 1.0 CB B:CYS65 3.6 45.1 1.0 CD B:CD301 3.6 49.0 1.0 OE2 B:GLU92 3.6 43.1 1.0 ND1 B:HIS67 4.4 57.0 1.0 CG B:HIS67 4.5 54.0 1.0 CG B:GLU92 4.7 43.7 1.0 O B:HOH430 4.7 54.4 1.0 CA B:CYS65 4.9 40.0 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