Iodine in PDB 3i6o: Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A

All present enzymatic activity of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A:
3.4.23.16;

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A, PDB code: 3i6o was solved by A.A.Chumanevich, Y.-F.Wang, A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.17
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.764, 86.328, 45.976, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.6

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A (pdb code 3i6o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A, PDB code: 3i6o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I211 b:15.2 occ:0.75 N A:THR74 3.6 11.2 1.0 ND2 A:ASN88 3.7 12.0 1.0 OG1 A:THR74 3.9 13.9 1.0 CA A:GLY73 4.1 12.8 1.0 CB A:THR74 4.1 11.8 1.0 CB A:ASN88 4.1 10.3 1.0 O A:HOH1032 4.4 17.0 1.0 C A:GLY73 4.4 11.7 1.0 CG A:ASN88 4.5 10.7 1.0 CA A:THR74 4.5 11.0 1.0 O A:ASN88 4.8 11.7 1.0

Iodine binding site 2 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I216 b:23.9 occ:0.40 O A:HOH1232 2.6 25.9 0.5 O A:HOH1133 3.3 33.8 1.0 N A:GLY48 3.6 12.1 1.0 C39 B:GR6301 4.0 16.2 0.5 CA A:ILE47 4.1 12.7 1.0 O A:GLY48 4.1 22.9 1.0 O A:HOH1154 4.2 32.4 0.5 CB A:ILE47 4.3 14.9 1.0 C30 B:GR6301 4.3 10.4 0.5 C29 B:GR6301 4.3 11.9 0.5 C A:ILE47 4.4 11.5 1.0 C26 B:GR6301 4.5 10.4 0.5 CA A:GLY48 4.5 13.3 1.0 CG2 A:ILE47 4.6 18.4 1.0 C41 B:GR6301 4.6 16.0 0.5 C2 B:GR6301 4.6 11.1 0.5 O A:HOH1159 4.7 35.8 1.0 C A:GLY48 4.8 15.0 1.0 O A:MET46 4.8 14.6 1.0 O27 B:GR6301 4.9 9.6 0.5 CE2 A:PHE53 5.0 14.5 1.0

Iodine binding site 3 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I217 b:30.0 occ:0.40 O A:THR12 3.5 17.1 1.0 N A:GLY68 3.6 21.8 1.0 O A:GLU65 3.9 17.9 1.0 N A:ALA67 4.0 17.9 1.0 C A:THR12 4.1 14.3 1.0 CB A:GLU65 4.1 20.2 1.0 N A:LYS14 4.2 14.5 1.0 OE2 A:GLU65 4.2 43.8 1.0 CA A:ILE13 4.2 14.1 1.0 C A:GLU65 4.2 16.5 1.0 C A:ILE13 4.2 13.6 1.0 CA A:GLY68 4.4 24.5 1.0 CA A:ALA67 4.4 21.1 1.0 N A:ILE13 4.4 13.6 1.0 CG2 A:THR12 4.4 21.0 1.0 C A:ALA67 4.5 21.4 1.0 CD A:GLU65 4.6 38.0 1.0 C A:ILE66 4.6 17.1 1.0 CB A:LYS14 4.6 17.3 1.0 N A:ILE66 4.6 15.8 1.0 CB A:THR12 4.7 19.0 1.0 O A:ILE13 4.8 15.2 1.0 CA A:ILE66 4.8 15.8 1.0 CA A:GLU65 4.8 15.7 1.0

Iodine binding site 4 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I220 b:26.1 occ:0.40 N A:THR12 3.5 15.3 1.0 O A:HOH1105 3.5 37.9 1.0 CB A:ALA67 3.9 26.1 1.0 CB A:VAL11 4.0 15.5 1.0 CA A:ALA67 4.0 21.1 1.0 CA A:VAL11 4.1 13.6 1.0 CB A:THR12 4.3 19.0 1.0 C A:VAL11 4.4 13.7 1.0 CG1 A:VAL11 4.4 19.9 1.0 OG1 A:THR12 4.4 22.9 1.0 CA A:THR12 4.4 15.0 1.0 O A:THR12 4.6 17.1 1.0 N A:ALA67 4.9 17.9 1.0

Iodine binding site 5 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I224 b:19.3 occ:0.50 I A:IOD225 2.3 28.3 0.2 O A:HOH1032 3.5 17.0 1.0 CG A:GLN61 3.7 23.8 1.0 CA A:GLN61 4.1 14.3 1.0 CG1 A:ILE72 4.3 15.6 1.0 CA A:GLY73 4.3 12.8 1.0 N A:GLN61 4.4 14.1 1.0 CB A:GLN61 4.4 17.6 1.0 CG2 A:ILE72 4.5 16.8 1.0 N A:GLY73 4.5 11.8 1.0 CD1 A:ILE72 4.5 17.2 1.0 NE2 A:GLN61 4.6 45.7 1.0 O A:ILE72 4.7 12.3 1.0 C A:ILE72 4.7 11.6 1.0 CD A:GLN61 4.7 31.0 1.0 CB A:ILE72 4.9 14.8 1.0 C A:GLY73 4.9 11.7 1.0

Iodine binding site 6 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I225 b:28.3 occ:0.20 I A:IOD224 2.3 19.3 0.5 CG2 A:ILE72 4.1 16.8 1.0 CD1 A:ILE72 4.1 17.2 1.0 CG A:GLN61 4.2 23.8 1.0 NE2 A:GLN61 4.3 45.7 1.0 CG1 A:ILE72 4.4 15.6 1.0 CD A:GLN61 4.7 31.0 1.0 CB A:ILE72 4.9 14.8 1.0

Iodine binding site 7 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I228 b:28.0 occ:0.30 O A:HOH1195 2.5 25.9 0.5 N A:LYS55 3.5 11.7 1.0 CA A:ILE54 3.9 11.7 1.0 CB A:ILE54 4.0 12.8 1.0 CG A:PRO79 4.1 15.1 1.0 O A:HOH1218 4.1 26.0 0.5 C A:ILE54 4.2 11.1 1.0 CB A:LYS55 4.2 13.3 1.0 CG2 A:ILE54 4.3 15.3 1.0 CA A:LYS55 4.4 10.9 1.0 O A:LYS55 4.5 12.4 1.0 O A:PHE53 4.8 14.5 1.0 CD A:PRO79 4.9 14.0 1.0 C A:LYS55 4.9 10.2 1.0

Iodine binding site 8 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ A:I229 b:30.4 occ:0.30 O A:HOH1047 3.5 20.0 1.0 N A:ILE63 3.7 16.4 1.0 CD1 A:ILE62 4.2 16.2 1.0 CA A:ILE62 4.2 13.3 1.0 CG2 A:ILE62 4.4 14.3 1.0 C A:ILE62 4.5 13.7 1.0 O A:GLN61 4.6 17.1 1.0 CB A:ILE63 4.6 20.5 1.0 O A:ILE63 4.6 18.6 1.0 CG A:PRO39 4.6 28.4 1.0 CA A:ILE63 4.6 16.9 1.0 CB A:ILE62 4.8 13.7 1.0 CG1 A:ILE63 4.8 22.3 1.0 CD A:PRO39 4.8 24.4 1.0 O A:HOH1229 5.0 35.5 1.0

Iodine binding site 9 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ B:I212 b:22.7 occ:0.50 O B:HOH1226 3.6 22.8 1.0 N B:THR112 3.6 11.9 1.0 CB B:VAL111 4.0 14.0 1.0 CA B:ALA167 4.1 14.7 1.0 CA B:VAL111 4.2 12.2 1.0 CB B:ALA167 4.2 17.3 1.0 CB B:THR112 4.2 13.8 1.0 OG1 B:THR112 4.4 17.5 1.0 C B:VAL111 4.4 11.4 1.0 CA B:THR112 4.4 11.5 1.0 CG1 B:VAL111 4.5 16.7 1.0 O B:THR112 4.5 13.1 1.0 C B:ALA167 5.0 15.2 1.0 N B:ALA167 5.0 13.1 1.0 C B:THR112 5.0 11.7 1.0

Iodine binding site 10 out of 19 in the Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Wild Type Hiv-1 Protease with Macrocyclic Inhibitor Grl-0216A within 5.0Å range: probe atom residue distance (Å) B Occ B:I213 b:22.1 occ:0.50 O B:HOH1124 2.7 19.7 0.5 CE B:LYS155 3.8 32.6 1.0 CB B:PRO144 3.8 15.9 0.4 CB B:PRO144 4.0 14.9 0.6 I B:IOD215 4.2 18.8 0.3 CG B:MET146 4.3 38.6 1.0 NZ B:LYS155 4.3 41.2 1.0 SD B:MET146 4.3 35.3 1.0 O B:PRO144 4.3 15.6 0.6 CG B:PRO144 4.3 15.4 0.6 C B:PRO144 4.4 14.9 0.6 CG B:PRO144 4.6 16.6 0.4 N B:LYS145 4.6 17.7 0.6 CD B:LYS155 4.8 27.9 1.0 CA B:PRO144 4.9 12.3 0.6 C B:LYS145 4.9 21.2 0.6 N B:LYS145 4.9 18.9 0.4 CG B:LYS155 4.9 25.1 1.0 CA B:PRO144 5.0 13.9 0.4

A.K.Ghosh, S.Kulkarni, D.D.Anderson, L.Hong, A.Baldridge, Y.F.Wang, A.A.Chumanevich, A.Y.Kovalevsky, Y.Tojo, M.Amano, Y.Koh, J.Tang, I.T.Weber, H.Mitsuya. Design, Synthesis, Protein-Ligand X-Ray Structure, and Biological Evaluation of A Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance. J.Med.Chem. V. 52 7689 2009.
ISSN: ISSN 0022-2623
PubMed: 19746963
DOI: 10.1021/JM900695W