Fluorine 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
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-(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 Fluorine atom.
In total 5 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-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide, PDB code: 7snl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 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 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-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:43.1 occ:1.00 F32 A:9VI301 0.0 43.1 1.0 C31 A:9VI301 1.4 41.5 1.0 C30 A:9VI301 2.3 42.5 1.0 C33 A:9VI301 2.4 34.8 1.0 O A:HOH406 3.0 22.8 1.0 O A:LEU56 3.1 22.2 1.0 CE A:MET66 3.2 19.8 1.0 CB A:MET66 3.3 23.7 1.0 C46 A:9VI301 3.5 37.8 1.0 C29 A:9VI301 3.6 41.6 1.0 C34 A:9VI301 3.6 36.4 1.0 CG A:MET66 3.8 26.1 1.0 C A:LEU56 3.8 20.7 1.0 C47 A:9VI301 4.1 41.6 1.0 CB A:LEU56 4.1 23.6 1.0 C36 A:9VI301 4.1 32.9 1.0 SD A:MET66 4.3 29.5 1.0 CA A:MET66 4.4 22.8 1.0 OD1 A:ASN57 4.4 31.9 1.0 CA A:LEU56 4.5 23.9 1.0 N A:ASN57 4.5 23.6 1.0 O A:MET66 4.5 27.1 1.0 CA A:ASN57 4.6 25.6 1.0 C A:MET66 4.8 27.2 1.0 F35 A:9VI301 4.8 59.5 1.0 C28 A:9VI301 4.8 47.2 1.0 C45 A:9VI301 4.9 48.2 1.0 OE1 A:GLN63 5.0 24.9 1.0

Fluorine binding site 2 out of 5 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 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-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:59.5 occ:1.00 F35 A:9VI301 0.0 59.5 1.0 C34 A:9VI301 1.4 36.4 1.0 C36 A:9VI301 2.4 32.9 1.0 C33 A:9VI301 2.4 34.8 1.0 C A:LEU69 3.2 27.2 1.0 N A:LYS70 3.2 27.9 1.0 O A:LEU69 3.3 28.2 1.0 CB A:LEU69 3.4 27.6 1.0 CD1 A:ILE73 3.4 26.7 1.0 CG A:LEU69 3.5 29.4 1.0 CA A:LYS70 3.5 28.2 1.0 C29 A:9VI301 3.6 41.6 1.0 C31 A:9VI301 3.6 41.5 1.0 O A:MET66 3.7 27.1 1.0 CD A:LYS70 3.7 33.1 1.0 CG A:LYS70 3.8 30.7 1.0 CD2 A:LEU69 3.8 26.2 1.0 CA A:LEU69 3.9 27.0 1.0 C30 A:9VI301 4.1 42.5 1.0 CB A:LYS70 4.2 31.1 1.0 CD1 A:LEU56 4.2 21.9 1.0 CG1 A:ILE73 4.4 27.7 1.0 F32 A:9VI301 4.8 43.1 1.0 C A:MET66 4.8 27.2 1.0 N A:LEU69 4.8 26.1 1.0 C A:LYS70 4.8 29.4 1.0 CD1 A:LEU69 4.9 26.2 1.0 C28 A:9VI301 4.9 47.2 1.0 CB A:ILE73 5.0 29.7 1.0

Fluorine binding site 3 out of 5 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 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-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:60.7 occ:1.00 F51 A:9VI301 0.0 60.7 1.0 C50 A:9VI301 1.3 50.1 1.0 F52 A:9VI301 2.2 56.4 1.0 F53 A:9VI301 2.2 44.9 1.0 C43 A:9VI301 2.4 52.2 1.0 N42 A:9VI301 3.0 56.2 1.0 C44 A:9VI301 3.5 50.9 1.0 O A:HOH478 3.7 47.1 1.0 C49 A:9VI301 4.2 46.7 1.0 N41 A:9VI301 4.2 52.4 1.0 C45 A:9VI301 4.5 48.2 1.0 NZ A:LYS70 4.9 39.1 1.0

Fluorine binding site 4 out of 5 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 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-(Trifluoromethyl)-4,5,6,7-Tetrahydro-1H-Indazol-1-Yl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:56.4 occ:1.00 F52 A:9VI301 0.0 56.4 1.0 C50 A:9VI301 1.4 50.1 1.0 F51 A:9VI301 2.2 60.7 1.0 F53 A:9VI301 2.2 44.9 1.0 C43 A:9VI301 2.4 52.2 1.0 C44 A:9VI301 2.9 50.9 1.0 C49 A:9VI301 2.9 46.7 1.0 N42 A:9VI301 3.7 56.2 1.0 C45 A:9VI301 4.2 48.2 1.0 C48 A:9VI301 4.4 42.0 1.0 N41 A:9VI301 4.5 52.4 1.0

Fluorine binding site 5 out of 5 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 Fluorine with other atoms in the F 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:F301 b:44.9 occ:1.00 F53 A:9VI301 0.0 44.9 1.0 C50 A:9VI301 1.4 50.1 1.0 F51 A:9VI301 2.2 60.7 1.0 F52 A:9VI301 2.2 56.4 1.0 C43 A:9VI301 2.3 52.2 1.0 N42 A:9VI301 2.9 56.2 1.0 C44 A:9VI301 3.6 50.9 1.0 N41 A:9VI301 4.1 52.4 1.0 C49 A:9VI301 4.3 46.7 1.0 C45 A:9VI301 4.5 48.2 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.