Iodine in PDB 7rmj: Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide

The structure of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide, PDB code: 7rmj was solved by S.M.Bester, M.Kvaratskhelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 2.27
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	160.023, 160.023, 57.598, 90, 90, 120
R / Rfree (%)	21.4 / 24.8

The structure of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide also contains other interesting chemical elements:

Fluorine	(F)	48 atoms
Chlorine	(Cl)	23 atoms

The binding sites of Iodine atom in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide (pdb code 7rmj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide, PDB code: 7rmj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:41.4 occ:1.00 N A:LYS158 3.7 43.0 1.0 N A:GLU159 3.8 40.4 1.0 CA A:GLY156 3.8 37.0 1.0 CD A:PRO157 3.9 43.8 1.0 N A:PRO157 4.0 41.8 1.0 C A:LYS158 4.0 46.4 1.0 C A:GLY156 4.0 40.8 1.0 CA A:LYS158 4.2 48.4 1.0 CB A:GLU159 4.2 40.6 1.0 CB A:LYS158 4.3 50.6 1.0 CA A:GLU159 4.3 38.3 1.0 CG A:PRO157 4.4 48.1 1.0 O A:LYS158 4.7 42.6 1.0 C A:PRO157 4.7 44.3 1.0 O A:GLY156 4.8 39.7 1.0 N A:GLY156 4.9 33.2 1.0 CA A:PRO157 4.9 44.3 1.0

Iodine binding site 2 out of 5 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:40.7 occ:1.00 CA B:GLY156 3.8 41.7 1.0 N B:LYS158 3.8 41.6 1.0 N B:GLU159 3.8 42.2 1.0 CD B:PRO157 3.9 42.5 1.0 C B:GLY156 4.0 41.8 1.0 C B:LYS158 4.1 45.1 1.0 N B:PRO157 4.1 41.5 1.0 CB B:GLU159 4.1 38.8 1.0 CA B:LYS158 4.3 48.5 1.0 CA B:GLU159 4.3 40.5 1.0 CB B:LYS158 4.4 52.2 1.0 CG B:PRO157 4.5 48.1 1.0 O B:LYS158 4.7 46.3 1.0 O B:GLY156 4.7 39.5 1.0 N B:GLY156 4.8 39.9 1.0 C B:PRO157 4.9 41.2 1.0

Iodine binding site 3 out of 5 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:80.8 occ:1.00 NH1 B:ARG18 3.3 72.7 1.0 CZ B:ARG18 4.0 77.0 1.0 NE B:ARG18 4.1 73.4 1.0 CB B:ALA22 4.7 23.8 1.0 O B:ARG18 4.9 26.5 1.0

Iodine binding site 4 out of 5 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ C:I302 b:35.6 occ:1.00 N C:LYS158 3.6 38.2 1.0 N C:GLU159 3.8 33.3 1.0 CA C:GLY156 3.8 33.3 1.0 CD C:PRO157 3.8 39.8 1.0 N C:PRO157 4.0 35.6 1.0 C C:LYS158 4.0 39.8 1.0 C C:GLY156 4.0 32.0 1.0 CA C:LYS158 4.1 38.9 1.0 CB C:LYS158 4.2 40.6 1.0 CB C:GLU159 4.2 29.1 1.0 CA C:GLU159 4.4 29.0 1.0 CG C:PRO157 4.4 36.8 1.0 O C:LYS158 4.7 41.6 1.0 C C:PRO157 4.7 35.6 1.0 O C:GLY156 4.8 31.3 1.0 N C:GLY156 4.9 31.8 1.0 CA C:PRO157 4.9 37.8 1.0

Iodine binding site 5 out of 5 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor (S)-N-(1-(3-(4-Chloro-3-(Methylsulfonamido)-1-(2,2,2-Trifluoroethyl)- 1H-Indazol-7-Yl)-6-(3-Methyl-3-(Methylsulfonyl)But-1-Yn-1-Yl)Pyridin- 2-Yl)-2-(3,5-Difluorophenyl)Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7- Tetrahydro-1H-Indazol-1-Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ C:I303 b:76.9 occ:1.00 O C:HOH434 3.7 31.3 1.0 CB C:ALA22 4.8 21.5 1.0 O C:HOH491 4.8 36.6 1.0 O C:ARG18 5.0 22.3 1.0

S.M.Bester, D.Adu-Ampratwum, A.S.Annamalai, G.Wei, L.Briganti, B.C.Murphy, R.Haney, J.R.Fuchs, M.Kvaratskhelia. Structural and Mechanistic Bases of Viral Resistance to Hiv-1 Capsid Inhibitor Lenacapavir. Mbio V. 13 80422 2022.
ISSN: ESSN 2150-7511
PubMed: 36190128
DOI: 10.1128/MBIO.01804-22