Chlorine in PDB 7snn: 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide, PDB code: 7snn 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)	36.07 / 2.37
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.272, 92.272, 57.87, 90, 90, 120
R / Rfree (%)	21.1 / 23.3

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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide also contains other interesting chemical elements:

Iodine	(I)	3 atoms
Fluorine	(F)	4 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide (pdb code 7snn). 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide, PDB code: 7snn:
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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:64.3 occ:1.00 CL12 A:9WW304 0.0 64.3 1.0 C11 A:9WW304 1.8 56.4 1.0 C13 A:9WW304 2.8 47.9 1.0 C10 A:9WW304 2.8 59.0 1.0 OD1 A:ASN74 3.0 47.6 1.0 N05 A:9WW304 3.2 65.7 1.0 C04 A:9WW304 3.3 62.2 1.0 O A:HOH456 3.5 37.3 1.0 CG2 A:ILE73 3.6 28.3 1.0 CG A:ASN74 3.6 41.8 1.0 O A:LYS70 3.7 34.4 1.0 CB A:ILE73 3.9 35.2 1.0 ND2 A:ASN74 4.0 42.2 1.0 C14 A:9WW304 4.1 48.7 1.0 C52 A:9WW304 4.1 58.9 1.0 N A:ASN74 4.2 34.3 1.0 CA A:LYS70 4.3 36.0 1.0 C A:LYS70 4.4 35.0 1.0 CB A:LYS70 4.5 36.7 1.0 C A:ILE73 4.6 34.9 1.0 C15 A:9WW304 4.6 51.5 1.0 N03 A:9WW304 4.6 65.1 1.0 CA A:ASN74 4.7 38.6 1.0 CB A:ASN74 4.7 37.4 1.0 S06 A:9WW304 4.8 88.1 1.0 CA A:ILE73 4.8 33.1 1.0 CD1 A:ILE73 4.9 32.5 1.0 CB A:ALA105 4.9 26.5 1.0 N02 A:9WW304 5.0 59.7 1.0 CG A:LYS70 5.0 38.8 1.0 OG1 A:THR107 5.0 46.1 1.0 CG1 A:ILE73 5.0 30.9 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:17.9 occ:1.00 N A:GLY61 3.6 35.4 1.0 CG A:GLN63 4.0 28.8 1.0 CA A:GLY60 4.0 31.1 1.0 CD A:GLN63 4.0 29.9 1.0 OE1 A:GLN63 4.2 27.5 1.0 C A:GLY60 4.3 36.1 1.0 NE2 A:GLN63 4.5 28.6 1.0 CA A:GLY61 4.6 31.4 1.0 O A:VAL59 4.9 28.9 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:47.6 occ:1.00 O A:HOH439 3.0 45.3 1.0 N A:ARG162 3.4 31.5 1.0 CB A:ARG162 3.6 36.6 1.0 N A:PHE161 3.7 32.2 1.0 CB A:PRO160 4.0 35.1 1.0 CA A:ARG162 4.1 30.4 1.0 CA A:GLN219 4.2 65.7 1.0 CL A:CL311 4.3 21.9 1.0 C A:PRO160 4.3 34.8 1.0 C A:PHE161 4.3 31.9 1.0 CA A:PHE161 4.3 30.1 1.0 CA A:PRO160 4.4 32.7 1.0 CG A:GLN219 4.4 86.9 1.0 CB A:PHE161 4.4 32.9 1.0 N A:GLY220 4.4 68.1 1.0 O A:CYS218 4.6 46.5 1.0 NE A:ARG162 4.6 47.8 1.0 CB A:GLN219 4.8 68.3 1.0 C A:GLN219 4.9 70.8 1.0 CG A:ARG162 5.0 41.5 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:49.9 occ:1.00 NH1 A:ARG167 3.2 29.5 1.0 O A:HOH497 3.2 37.6 1.0 CD1 A:ILE153 3.6 31.2 1.0 CD A:ARG167 3.9 33.7 1.0 O A:HOH475 4.2 43.3 1.0 CB A:ARG167 4.3 27.9 1.0 CZ A:ARG167 4.3 31.3 1.0 CG A:ARG167 4.4 28.5 1.0 NE A:ARG167 4.5 31.6 1.0 OG1 A:THR171 4.8 25.9 1.0 OG1 A:THR148 4.9 47.6 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:24.0 occ:1.00 O A:GLY60 2.8 34.9 1.0 O A:HOH465 3.1 34.5 1.0 CD2 A:HIS62 3.6 31.4 1.0 CG A:GLU28 3.7 43.3 1.0 O A:HOH409 3.7 48.2 1.0 NE2 A:HIS62 4.0 40.4 1.0 C A:GLY60 4.0 36.1 1.0 CG1 A:VAL27 4.1 29.5 1.0 CA A:GLU28 4.1 36.2 1.0 N A:GLU28 4.3 31.0 1.0 CB A:GLU28 4.4 36.7 1.0 O A:VAL27 4.4 33.9 1.0 C A:VAL27 4.5 33.9 1.0 CG1 A:VAL59 4.5 26.0 1.0 N A:GLY60 4.6 37.7 1.0 CD A:GLU28 4.8 44.0 1.0 CB A:VAL27 4.8 25.4 1.0 CA A:GLY60 4.8 31.1 1.0 CG A:HIS62 4.9 37.9 1.0 OE2 A:GLU28 4.9 56.2 1.0 N A:GLY61 5.0 35.4 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:48.9 occ:1.00 CD1 A:ILE124 3.8 48.7 1.0 O A:HOH412 4.0 52.1 1.0 CG2 A:ILE124 4.1 42.0 1.0 CH2 A:TRP80 4.3 35.6 1.0 CD A:PRO125 4.4 37.2 1.0 O A:HOH511 4.5 38.4 1.0 CD1 A:ILE129 4.5 25.5 1.0 CA A:ILE124 4.6 42.0 1.0 CB A:ILE124 4.7 38.4 1.0 CG1 A:ILE124 4.8 43.5 1.0 CZ2 A:TRP80 4.9 33.9 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:27.0 occ:1.00 CD A:PRO17 3.6 28.2 1.0 N A:ARG18 3.7 33.1 1.0 O A:HOH514 3.9 53.8 1.0 CB A:ARG18 3.9 29.8 1.0 CB A:SER16 4.0 26.9 1.0 N A:PRO17 4.1 31.5 1.0 CG A:PRO17 4.2 29.6 1.0 CB A:PRO17 4.3 29.0 1.0 CA A:ARG18 4.4 30.3 1.0 OG A:SER16 4.5 36.1 1.0 C A:PRO17 4.6 30.0 1.0 CA A:PRO17 4.6 29.2 1.0 C A:SER16 4.7 30.7 1.0 CA A:SER16 4.8 28.4 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H)- Yl)Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:21.9 occ:1.00 CD A:GLN219 3.6 96.4 1.0 NE A:ARG162 3.6 47.8 1.0 NH2 A:ARG162 3.7 52.8 1.0 NE2 A:GLN219 3.7 93.7 1.0 CE A:MET215 3.8 33.0 1.0 CG A:GLN219 3.8 86.9 1.0 OE1 A:GLN219 3.9 92.3 1.0 CZ A:ARG162 4.1 53.5 1.0 CL A:CL306 4.3 47.6 1.0 O A:MET215 4.4 43.0 1.0 CB A:ARG162 4.4 36.6 1.0 CB A:GLN219 4.5 68.3 1.0 CB A:MET215 4.6 35.7 1.0 CG A:ARG162 4.7 41.5 1.0 CD A:ARG162 4.8 47.7 1.0 C A:MET215 4.8 43.7 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-(Difluoromethyl)-5,6-Dihydrocyclopenta[C]Pyrazol-1(4H) -Yl)Acetamide To Be Published.