Chlorine in PDB 7snl: Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-2-Yl)-2-(3,5-Difluorophenyl) Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide, PDB code: 7snl 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)	46.93 / 2.39
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.26, 92.26, 57.98, 90, 90, 120
R / Rfree (%)	24.3 / 26.1

The structure of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:

Iodine	(I)	4 atoms
Fluorine	(F)	5 atoms

The binding sites of Chlorine atom in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-2-Yl)-2-(3,5-Difluorophenyl) Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide (pdb code 7snl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-2-Yl)-2-(3,5-Difluorophenyl) Ethyl)-2-(3-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide, PDB code: 7snl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 1 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl301 b:60.9 occ:1.00 CL12 A:9VI301 0.0 60.9 1.0 C11 A:9VI301 1.8 59.2 1.0 C10 A:9VI301 2.7 56.4 1.0 C13 A:9VI301 2.8 48.3 1.0 OD1 A:ASN74 2.9 37.9 1.0 N05 A:9VI301 3.0 64.5 1.0 C04 A:9VI301 3.2 59.8 1.0 O A:HOH456 3.4 37.0 1.0 CG A:ASN74 3.5 32.0 1.0 ND2 A:ASN74 3.7 37.1 1.0 CG2 A:ILE73 3.8 24.3 1.0 O A:LYS70 3.8 28.6 1.0 C54 A:9VI301 4.1 54.5 1.0 C14 A:9VI301 4.1 52.5 1.0 CB A:ILE73 4.1 29.7 1.0 N A:ASN74 4.2 31.0 1.0 N03 A:9VI301 4.5 65.1 1.0 CE A:LYS70 4.5 40.7 1.0 S06 A:9VI301 4.5 86.6 1.0 CB A:ASN74 4.6 30.2 1.0 CA A:ASN74 4.6 29.3 1.0 C15 A:9VI301 4.6 54.9 1.0 C A:LYS70 4.6 29.4 1.0 CA A:LYS70 4.6 28.2 1.0 C A:ILE73 4.6 30.3 1.0 O09 A:9VI301 4.8 81.9 1.0 CD A:LYS70 4.8 33.1 1.0 CB A:LYS70 4.9 31.1 1.0 N02 A:9VI301 4.9 54.5 1.0 CA A:ILE73 5.0 27.9 1.0

Chlorine binding site 2 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 2 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl306 b:18.3 occ:1.00 N A:GLY61 3.4 36.1 1.0 CA A:GLY60 3.9 29.8 1.0 CD A:GLN63 4.1 26.9 1.0 CG A:GLN63 4.1 31.3 1.0 C A:GLY60 4.2 34.4 1.0 OE1 A:GLN63 4.2 24.9 1.0 CA A:GLY61 4.4 31.5 1.0 NE2 A:GLN63 4.5 27.1 1.0 O A:VAL59 4.8 26.8 1.0

Chlorine binding site 3 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 3 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl307 b:39.6 occ:1.00 N A:ARG162 3.5 30.4 1.0 CB A:ARG162 3.7 35.3 1.0 CB A:PRO160 3.8 34.2 1.0 N A:PHE161 3.8 32.0 1.0 C A:PRO160 4.3 31.9 1.0 CA A:ARG162 4.3 28.8 1.0 CA A:PRO160 4.3 35.2 1.0 CA A:GLN219 4.3 50.4 1.0 I A:IOD304 4.3 77.1 1.0 N A:GLY220 4.4 54.5 1.0 CA A:PHE161 4.5 29.9 1.0 C A:PHE161 4.5 28.9 1.0 O A:CYS218 4.5 42.9 1.0 CB A:PHE161 4.6 28.4 1.0 CG A:GLN219 4.8 49.3 1.0 NE A:ARG162 4.9 39.5 1.0 CB A:GLN219 4.9 50.8 1.0 C A:GLN219 4.9 47.5 1.0

Chlorine binding site 4 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 4 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl308 b:42.5 occ:1.00 O A:HOH484 3.2 41.8 1.0 NH1 A:ARG167 3.2 30.7 1.0 CD1 A:ILE153 3.6 32.8 1.0 CD A:ARG167 3.9 31.9 1.0 CL A:CL309 4.3 66.7 1.0 CZ A:ARG167 4.3 29.7 1.0 CB A:ARG167 4.4 25.9 1.0 CG A:ARG167 4.5 26.6 1.0 NE A:ARG167 4.6 29.5 1.0 OG1 A:THR148 4.7 39.8 1.0 OG1 A:THR171 4.9 31.4 1.0

Chlorine binding site 5 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 5 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl309 b:66.7 occ:1.00 O A:HOH420 3.7 26.9 1.0 O A:ASP152 3.9 35.1 1.0 CG2 A:THR148 4.0 35.7 1.0 CL A:CL308 4.3 42.5 1.0 CD1 A:ILE153 4.6 32.8 1.0 OG1 A:THR148 4.7 39.8 1.0 CB A:ASP152 4.7 38.8 1.0 C A:ASP152 4.7 31.4 1.0 NH1 A:ARG167 5.0 30.7 1.0 CB A:THR148 5.0 38.6 1.0

Chlorine binding site 6 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 6 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl310 b:18.6 occ:1.00 O A:GLY60 2.8 35.1 1.0 O A:HOH437 2.8 29.1 1.0 CD2 A:HIS62 3.5 26.9 1.0 CG A:GLU28 3.8 31.1 1.0 NE2 A:HIS62 3.8 33.1 1.0 C A:GLY60 4.0 34.4 1.0 CA A:GLU28 4.1 32.1 1.0 CG1 A:VAL27 4.1 25.8 1.0 N A:GLU28 4.3 28.3 1.0 O A:VAL27 4.3 29.2 1.0 C A:VAL27 4.4 29.0 1.0 CG1 A:VAL59 4.5 23.3 1.0 CB A:GLU28 4.5 33.5 1.0 N A:GLY60 4.5 31.4 1.0 CB A:VAL27 4.7 22.1 1.0 CG A:HIS62 4.7 32.1 1.0 CA A:GLY60 4.8 29.8 1.0 CD A:GLU28 5.0 34.0 1.0

Chlorine binding site 7 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 7 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl311 b:47.5 occ:1.00 CD1 A:ILE124 3.9 42.6 1.0 CG2 A:ILE124 4.1 39.2 1.0 O A:HOH518 4.2 35.4 1.0 CD A:PRO125 4.4 39.5 1.0 CD1 A:ILE129 4.5 29.6 1.0 CH2 A:TRP80 4.5 36.4 1.0 CA A:ILE124 4.7 41.9 1.0 CB A:ILE124 4.8 37.5 1.0 CG1 A:ILE124 4.9 43.0 1.0

Chlorine binding site 8 out of 8 in the Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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 Chlorine with other atoms in the Cl binding site number 8 of Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido)-1H-Indazol-7-Yl)-4- Oxo-3,4-Dihydropyrido[2,3-D]Pyrimidin-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:Cl312 b:22.8 occ:1.00 CG A:ARG18 3.3 33.2 1.0 CD A:PRO17 3.5 30.2 1.0 N A:ARG18 3.9 28.4 1.0 CB A:SER16 4.0 29.0 1.0 N A:PRO17 4.0 28.9 1.0 CB A:ARG18 4.1 26.3 1.0 CG A:PRO17 4.1 29.6 1.0 O A:HOH517 4.2 57.2 1.0 CB A:PRO17 4.3 31.3 1.0 O A:HOH521 4.4 43.7 1.0 CA A:PRO17 4.6 30.9 1.0 CA A:ARG18 4.6 27.6 1.0 OG A:SER16 4.7 33.0 1.0 C A:PRO17 4.7 26.9 1.0 C A:SER16 4.7 29.5 1.0 CA A:SER16 4.7 27.4 1.0

D.Adu-Ampratwum, R.Haney, S.M.Bester, A.S.Annamalai, G.Wei, J.R.Fuchs, M.Kvaratskhelia. Disulfide Stabilized Hiv-1 Ca Hexamer in Complex with Capsid Inhibitor N-(1-(3-(4-Chloro-1-Methyl-3-(Methylsulfonamido) -1H-Indazol-7-Yl)-4-Oxo-3,4-Dihydropyrido[2, 3-D]Pyrimidin-2-Yl)-2-(3,5-Difluorophenyl)Ethyl) -2-(3-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide To Be Published.