Fluorine 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
Chlorine	(Cl)	8 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F304 b:49.9 occ:1.00 F32 A:9WW304 0.0 49.9 1.0 C31 A:9WW304 1.4 38.0 1.0 C33 A:9WW304 2.4 34.9 1.0 C30 A:9WW304 2.4 35.3 1.0 N A:LYS70 3.0 31.6 1.0 C A:LEU69 3.1 30.8 1.0 CD1 A:ILE73 3.2 32.5 1.0 CB A:LEU69 3.3 28.7 1.0 CA A:LYS70 3.3 36.0 1.0 CG A:LYS70 3.4 38.8 1.0 O A:LEU69 3.4 30.5 1.0 CG A:LEU69 3.5 34.1 1.0 C34 A:9WW304 3.6 42.9 1.0 C29 A:9WW304 3.6 44.3 1.0 O A:MET66 3.7 29.9 1.0 CA A:LEU69 3.8 30.6 1.0 CD2 A:LEU69 3.9 30.8 1.0 CB A:LYS70 3.9 36.7 1.0 C36 A:9WW304 4.1 44.5 1.0 CD1 A:LEU56 4.2 28.3 1.0 CG1 A:ILE73 4.2 30.9 1.0 C A:LYS70 4.7 35.0 1.0 N A:LEU69 4.7 29.1 1.0 CD A:LYS70 4.7 41.0 1.0 F35 A:9WW304 4.8 42.8 1.0 C A:MET66 4.8 30.2 1.0 CB A:ILE73 4.8 35.2 1.0 C28 A:9WW304 4.9 37.2 1.0 CD1 A:LEU69 4.9 33.7 1.0

Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F 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:F304 b:42.8 occ:1.00 F35 A:9WW304 0.0 42.8 1.0 C34 A:9WW304 1.4 42.9 1.0 C36 A:9WW304 2.4 44.5 1.0 C33 A:9WW304 2.4 34.9 1.0 CE A:MET66 3.1 27.5 1.0 CB A:MET66 3.1 27.4 1.0 O A:HOH415 3.2 29.5 1.0 O A:LEU56 3.4 27.1 1.0 C49 A:9WW304 3.5 41.2 1.0 CG A:MET66 3.6 30.4 1.0 C29 A:9WW304 3.6 44.3 1.0 C31 A:9WW304 3.7 38.0 1.0 C A:LEU56 4.0 25.7 1.0 CB A:LEU56 4.1 30.6 1.0 CA A:MET66 4.1 28.9 1.0 C30 A:9WW304 4.1 35.3 1.0 SD A:MET66 4.1 35.7 1.0 O A:MET66 4.3 29.9 1.0 C A:MET66 4.5 30.2 1.0 OD1 A:ASN57 4.5 35.2 1.0 C50 A:9WW304 4.5 40.5 1.0 CA A:LEU56 4.6 31.1 1.0 C48 A:9WW304 4.6 45.9 1.0 C38 A:9WW304 4.6 49.3 1.0 N A:ASN57 4.7 26.7 1.0 C40 A:9WW304 4.8 48.6 1.0 F32 A:9WW304 4.8 49.9 1.0 CA A:ASN57 4.9 30.5 1.0 O39 A:9WW304 4.9 51.5 1.0 C28 A:9WW304 4.9 37.2 1.0 N37 A:9WW304 4.9 48.1 1.0 OE1 A:GLN63 5.0 27.5 1.0

Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F 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:F304 b:48.4 occ:1.00 F45 A:9WW304 0.0 48.4 1.0 C44 A:9WW304 1.4 51.4 1.0 F46 A:9WW304 2.2 52.9 1.0 C43 A:9WW304 2.4 52.1 1.0 C47 A:9WW304 2.9 48.3 1.0 C51 A:9WW304 3.2 44.1 1.0 N42 A:9WW304 3.7 54.0 1.0 C48 A:9WW304 4.2 45.9 1.0 N41 A:9WW304 4.5 49.4 1.0 C50 A:9WW304 4.7 40.5 1.0 OE1 A:GLN67 4.7 39.7 1.0 NZ A:LYS70 4.8 52.6 1.0

Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F 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:F304 b:52.9 occ:1.00 F46 A:9WW304 0.0 52.9 1.0 C44 A:9WW304 1.4 51.4 1.0 F45 A:9WW304 2.2 48.4 1.0 C43 A:9WW304 2.4 52.1 1.0 N42 A:9WW304 3.0 54.0 1.0 C47 A:9WW304 3.6 48.3 1.0 N41 A:9WW304 4.2 49.4 1.0 C48 A:9WW304 4.5 45.9 1.0 C51 A:9WW304 4.6 44.1 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.