Fluorine in PDB 7k5m: Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution

The structure of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution, PDB code: 7k5m was solved by S.D.Kuduk, B.Stoops, R.Alexander, A.M.Lam, C.Espiritu, R.Vogel, V.Lau, K.Klumpp, O.A.Flores, G.D.Hartman, C.M.Lukacs, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.04 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.58, 87.96, 106.71, 90, 103.53, 90
R / Rfree (%)	24.2 / 27.6

The structure of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution (pdb code 7k5m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution, PDB code: 7k5m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:74.8 occ:1.00 F09 A:VXJ201 0.0 74.8 1.0 C08 A:VXJ201 1.4 64.3 1.0 C10 A:VXJ201 2.4 55.8 1.0 C06 A:VXJ201 2.4 69.4 1.0 CL07 A:VXJ201 3.0 62.0 0.8 CD2 A:LEU30 3.2 53.9 1.0 CG2 A:ILE105 3.2 55.3 1.0 C05 A:VXJ201 3.6 73.1 1.0 C11 A:VXJ201 3.6 55.8 1.0 CB A:ILE105 3.7 54.6 1.0 CD1 A:ILE105 3.7 48.2 1.0 CG2 A:THR33 4.0 49.2 1.0 CB A:THR33 4.1 48.2 1.0 C04 A:VXJ201 4.1 60.6 1.0 CG1 A:ILE105 4.3 48.6 1.0 OG1 A:THR33 4.4 49.1 1.0 CG A:LEU30 4.6 60.4 1.0 CD1 A:TRP102 4.6 41.1 1.0 CA A:LEU30 4.7 63.8 1.0 CA A:TRP102 4.7 57.5 1.0 CB A:LEU30 4.9 69.3 1.0 OG A:SER106 4.9 49.1 1.0 O A:LEU30 5.0 62.4 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:57.0 occ:1.00 F09 B:VXJ201 0.0 57.0 1.0 C08 B:VXJ201 1.4 57.9 1.0 C06 B:VXJ201 2.4 58.7 1.0 C10 B:VXJ201 2.4 55.8 1.0 CL07 B:VXJ201 3.0 55.8 0.7 CG2 B:ILE105 3.2 58.1 1.0 CD2 B:LEU30 3.2 61.8 1.0 C05 B:VXJ201 3.6 62.1 1.0 CB B:ILE105 3.6 60.6 1.0 C11 B:VXJ201 3.6 55.8 1.0 CD1 B:ILE105 3.7 62.0 1.0 C04 B:VXJ201 4.1 56.1 1.0 CG2 B:THR33 4.2 65.2 1.0 CG1 B:ILE105 4.3 61.2 1.0 CB B:THR33 4.3 64.7 1.0 CD1 B:TRP102 4.5 58.0 1.0 CA B:TRP102 4.6 66.1 1.0 OG1 B:THR33 4.6 64.9 1.0 CG B:LEU30 4.6 64.5 1.0 CA B:LEU30 4.8 68.3 1.0 OG B:SER106 4.9 61.3 1.0 O B:TRP102 4.9 59.9 1.0 CB B:LEU30 5.0 69.0 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:F500 b:64.4 occ:1.00 F09 C:VXJ500 0.0 64.4 1.0 C08 C:VXJ500 1.4 66.5 1.0 C10 C:VXJ500 2.4 57.0 1.0 C06 C:VXJ500 2.4 78.2 1.0 CL07 C:VXJ500 3.0 78.0 0.8 CD2 C:LEU30 3.2 76.2 1.0 CG2 C:ILE105 3.2 74.5 1.0 CD1 C:ILE105 3.6 67.2 1.0 CB C:ILE105 3.6 81.5 1.0 C05 C:VXJ500 3.6 72.4 1.0 C11 C:VXJ500 3.6 55.8 1.0 C04 C:VXJ500 4.1 60.3 1.0 CG2 C:THR33 4.2 66.6 1.0 CG1 C:ILE105 4.2 67.0 1.0 CB C:THR33 4.4 65.6 1.0 CA C:TRP102 4.5 76.5 1.0 CD1 C:TRP102 4.6 65.1 1.0 CG C:LEU30 4.6 77.4 1.0 OG1 C:THR33 4.8 66.3 1.0 CA C:LEU30 4.8 71.5 1.0 O C:LEU101 4.9 66.0 1.0 CB C:LEU30 4.9 81.4 1.0 O C:TRP102 4.9 64.6 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:67.1 occ:1.00 F09 D:VXJ201 0.0 67.1 1.0 C08 D:VXJ201 1.4 57.8 1.0 C10 D:VXJ201 2.4 55.8 1.0 C06 D:VXJ201 2.4 63.2 1.0 CL07 D:VXJ201 3.0 58.4 0.7 CD2 D:LEU30 3.2 69.8 1.0 CG2 D:ILE105 3.3 69.9 1.0 CD1 D:ILE105 3.5 54.7 1.0 CB D:ILE105 3.6 67.5 1.0 C05 D:VXJ201 3.6 61.5 1.0 C11 D:VXJ201 3.6 55.8 1.0 CG2 D:THR33 4.1 65.8 1.0 C04 D:VXJ201 4.1 58.6 1.0 CB D:THR33 4.1 65.7 1.0 CG1 D:ILE105 4.1 54.8 1.0 OG1 D:THR33 4.4 65.9 1.0 CA D:TRP102 4.5 65.6 1.0 CG D:LEU30 4.6 69.8 1.0 CA D:LEU30 4.6 64.6 1.0 CD1 D:TRP102 4.6 58.2 1.0 CB D:LEU30 4.8 73.8 1.0 O D:LEU30 4.8 66.5 1.0 O D:LEU101 4.9 54.2 1.0 O D:TRP102 5.0 62.4 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:F201 b:71.5 occ:1.00 F09 E:VXJ201 0.0 71.5 1.0 C08 E:VXJ201 1.4 64.3 1.0 C10 E:VXJ201 2.4 55.8 1.0 C06 E:VXJ201 2.4 72.0 1.0 CL07 E:VXJ201 3.0 65.1 0.8 CG2 E:ILE105 3.2 40.8 1.0 CD2 E:LEU30 3.4 64.0 1.0 CD1 E:ILE105 3.6 41.9 1.0 CB E:ILE105 3.6 61.2 1.0 C05 E:VXJ201 3.6 71.2 1.0 C11 E:VXJ201 3.6 55.8 1.0 CG2 E:THR33 4.1 61.1 1.0 C04 E:VXJ201 4.1 58.5 1.0 CG1 E:ILE105 4.2 42.0 1.0 CB E:THR33 4.2 60.6 1.0 CD1 E:TRP102 4.5 46.5 1.0 CA E:TRP102 4.5 51.2 1.0 OG1 E:THR33 4.6 60.9 1.0 CG E:LEU30 4.8 60.7 1.0 OG E:SER106 4.9 40.6 1.0 CA E:LEU30 4.9 71.2 1.0 O E:TRP102 4.9 43.1 1.0 CA E:ILE105 5.0 55.3 1.0 O E:LEU101 5.0 59.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:F500 b:55.8 occ:1.00 F09 F:VXJ500 0.0 55.8 1.0 C08 F:VXJ500 1.4 57.8 1.0 C10 F:VXJ500 2.4 55.8 1.0 C06 F:VXJ500 2.4 70.0 1.0 CL07 F:VXJ500 3.0 63.0 0.7 CD2 F:LEU30 3.3 57.3 1.0 CG2 F:ILE105 3.3 50.3 1.0 C05 F:VXJ500 3.6 69.2 1.0 C11 F:VXJ500 3.6 55.8 1.0 CB F:ILE105 3.7 49.0 1.0 CD1 F:ILE105 3.9 53.6 1.0 C04 F:VXJ500 4.1 57.5 1.0 CG2 F:THR33 4.3 60.2 1.0 CD1 F:TRP102 4.4 44.6 1.0 CG1 F:ILE105 4.4 48.9 1.0 CB F:THR33 4.5 59.6 1.0 CA F:TRP102 4.5 50.7 1.0 OG1 F:THR33 4.7 60.3 1.0 OG F:SER106 4.7 47.0 1.0 CG F:LEU30 4.7 64.0 1.0 O F:TRP102 4.8 50.0 1.0 CA F:LEU30 5.0 65.6 1.0

S.D.Kuduk, B.Stoops, R.Alexander, A.M.Lam, C.Espiritu, R.Vogel, V.Lau, K.Klumpp, O.A.Flores, G.D.Hartman. Identification of A New Class of Hbv Capsid Assembly Modulator. Bioorg.Med.Chem.Lett. V. 39 27848 2021.
ISSN: ESSN 1464-3405
PubMed: 33610748
DOI: 10.1016/J.BMCL.2021.127848