Fluorine in PDB 5t2p: Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01), PDB code: 5t2p was solved by Z.Zhou, Z.H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.04 / 1.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.927, 68.048, 85.703, 68.49, 69.99, 83.49
R / Rfree (%)	18 / 20.8

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine atom in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) (pdb code 5t2p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01), PDB code: 5t2p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:28.9 occ:1.00 F16 A:K89201 0.0 28.9 1.0 C14 A:K89201 1.3 26.5 1.0 C13 A:K89201 2.4 28.7 1.0 C15 A:K89201 2.4 22.8 1.0 F17 A:K89201 2.8 29.2 1.0 CG2 A:ILE105 3.2 37.8 1.0 OG A:SER106 3.3 28.0 1.0 CB A:ILE105 3.5 34.8 1.0 C12 A:K89201 3.6 24.5 1.0 C10 A:K89201 3.6 22.5 1.0 CD1 A:TRP102 3.7 28.9 1.0 CD2 A:LEU30 3.7 27.8 1.0 O A:TRP102 4.0 25.6 1.0 CA A:TRP102 4.1 22.6 1.0 N A:SER106 4.1 28.9 1.0 C11 A:K89201 4.1 22.5 1.0 CG A:TRP102 4.3 27.0 1.0 C A:ILE105 4.4 30.6 1.0 NE1 A:TRP102 4.4 24.4 1.0 CD1 A:ILE105 4.4 30.7 1.0 C A:TRP102 4.5 28.6 1.0 CA A:ILE105 4.5 28.6 1.0 CB A:SER106 4.5 29.3 1.0 CG1 A:ILE105 4.5 30.4 1.0 CA A:SER106 4.6 26.7 1.0 CB A:TRP102 4.6 23.5 1.0 F18 A:K89201 4.7 27.3 1.0 O A:LEU101 4.8 27.1 1.0 N09 A:K89201 4.8 23.7 1.0 O08 A:K89201 4.9 30.3 1.0 CG2 A:THR33 4.9 31.3 1.0

Fluorine binding site 2 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:29.2 occ:1.00 F17 A:K89201 0.0 29.2 1.0 C13 A:K89201 1.3 28.7 1.0 C12 A:K89201 2.3 24.5 1.0 C14 A:K89201 2.4 26.5 1.0 F18 A:K89201 2.7 27.3 1.0 F16 A:K89201 2.8 28.9 1.0 CD2 A:LEU30 3.1 27.8 1.0 CB A:THR33 3.2 30.2 1.0 OG1 A:THR33 3.3 27.9 1.0 CG2 A:THR33 3.4 31.3 1.0 CA A:LEU30 3.5 22.7 1.0 C11 A:K89201 3.6 22.5 1.0 C15 A:K89201 3.7 22.8 1.0 O A:ASP29 3.9 27.7 1.0 CG A:LEU30 4.1 22.8 1.0 CG2 A:ILE105 4.1 37.8 1.0 CD1 A:ILE105 4.1 30.7 1.0 O A:LEU30 4.1 29.4 1.0 C10 A:K89201 4.2 22.5 1.0 CB A:LEU30 4.2 20.9 1.0 N A:LEU30 4.3 26.0 1.0 C A:LEU30 4.3 23.0 1.0 C A:ASP29 4.4 25.7 1.0 CG A:PRO25 4.5 24.7 1.0 CA A:THR33 4.6 27.4 1.0 CB A:ILE105 4.7 34.8 1.0 CB A:PRO25 4.9 25.1 1.0 CG1 A:ILE105 5.0 30.4 1.0

Fluorine binding site 3 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:27.3 occ:1.00 F18 A:K89201 0.0 27.3 1.0 C12 A:K89201 1.3 24.5 1.0 C13 A:K89201 2.3 28.7 1.0 C11 A:K89201 2.3 22.5 1.0 F17 A:K89201 2.7 29.2 1.0 OG1 A:THR33 3.1 27.9 1.0 C14 A:K89201 3.6 26.5 1.0 C10 A:K89201 3.6 22.5 1.0 O A:ASP29 3.9 27.7 1.0 CG A:PRO25 3.9 24.7 1.0 CB A:THR33 4.0 30.2 1.0 C15 A:K89201 4.1 22.8 1.0 CB A:PRO25 4.1 25.1 1.0 CG2 A:THR33 4.3 31.3 1.0 C A:ASP29 4.4 25.7 1.0 CB A:ASP29 4.6 25.0 1.0 F16 A:K89201 4.7 28.9 1.0 N09 A:K89201 4.7 23.7 1.0 CD2 A:LEU30 4.8 27.8 1.0 N A:LEU30 4.8 26.0 1.0 CA A:LEU30 4.9 22.7 1.0

Fluorine binding site 4 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:33.5 occ:1.00 F29 A:K89201 0.0 33.5 1.0 C03 A:K89201 1.3 32.7 1.0 C04 A:K89201 2.3 22.7 1.0 C02 A:K89201 2.3 23.1 1.0 O20 A:K89201 2.8 29.0 1.0 S19 A:K89201 3.0 27.3 1.0 O A:HOH339 3.0 41.3 1.0 C23 A:K89201 3.4 36.4 1.0 C05 A:K89201 3.5 24.4 1.0 N22 A:K89201 3.5 25.4 1.0 C01 A:K89201 3.6 24.8 1.0 C06 A:K89201 4.1 27.1 1.0 O21 A:K89201 4.3 28.4 1.0 CB A:LEU140 4.5 47.7 1.0 C27 A:K89201 4.6 33.2 1.0 N A:LEU140 4.8 43.6 1.0 OH A:TYR118 4.9 30.7 1.0 O A:HOH398 4.9 49.9 1.0 C24 A:K89201 4.9 36.1 1.0 CD2 A:LEU140 5.0 62.8 1.0

Fluorine binding site 5 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:26.1 occ:1.00 F16 B:K89201 0.0 26.1 1.0 C14 B:K89201 1.3 22.5 1.0 C13 B:K89201 2.4 27.6 1.0 C15 B:K89201 2.4 24.2 1.0 F17 B:K89201 2.8 27.7 1.0 CG2 B:ILE105 3.2 26.4 1.0 CB B:ILE105 3.5 23.8 1.0 OG B:SER106 3.5 19.5 0.6 C12 B:K89201 3.6 22.3 1.0 CD1 B:TRP102 3.7 22.5 1.0 CD2 B:LEU30 3.7 28.4 1.0 C10 B:K89201 3.7 22.9 1.0 O B:TRP102 4.1 24.4 1.0 C11 B:K89201 4.1 19.2 1.0 CA B:TRP102 4.2 20.7 1.0 N B:SER106 4.3 23.6 0.4 N B:SER106 4.3 23.5 0.6 CD1 B:ILE105 4.3 21.9 1.0 NE1 B:TRP102 4.4 21.7 1.0 CG B:TRP102 4.4 22.9 1.0 CG1 B:ILE105 4.5 23.6 1.0 C B:ILE105 4.5 24.6 1.0 C B:TRP102 4.6 25.1 1.0 CA B:ILE105 4.6 25.2 1.0 CB B:TRP102 4.7 19.8 1.0 CB B:SER106 4.7 22.3 0.6 F18 B:K89201 4.7 26.8 1.0 CB B:SER106 4.8 22.3 0.4 CA B:SER106 4.8 22.9 0.6 CA B:SER106 4.8 23.2 0.4 CG2 B:THR33 4.8 23.5 1.0 N09 B:K89201 4.8 22.8 1.0 O08 B:K89201 4.9 24.3 1.0 O B:LEU101 4.9 24.3 1.0

Fluorine binding site 6 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:27.7 occ:1.00 F17 B:K89201 0.0 27.7 1.0 C13 B:K89201 1.3 27.6 1.0 C12 B:K89201 2.4 22.3 1.0 C14 B:K89201 2.4 22.5 1.0 F16 B:K89201 2.8 26.1 1.0 F18 B:K89201 2.8 26.8 1.0 CB B:THR33 3.1 25.3 1.0 CD2 B:LEU30 3.1 28.4 1.0 OG1 B:THR33 3.3 24.9 1.0 CG2 B:THR33 3.4 23.5 1.0 CA B:LEU30 3.5 19.9 1.0 C11 B:K89201 3.7 19.2 1.0 C15 B:K89201 3.7 24.2 1.0 O B:ASP29 3.9 21.2 1.0 CG B:LEU30 4.0 23.7 1.0 CD1 B:ILE105 4.1 21.9 1.0 O B:LEU30 4.1 22.1 1.0 CG2 B:ILE105 4.2 26.4 1.0 CB B:LEU30 4.2 18.9 1.0 C10 B:K89201 4.2 22.9 1.0 N B:LEU30 4.3 21.9 1.0 C B:LEU30 4.3 21.8 1.0 C B:ASP29 4.4 26.6 1.0 CA B:THR33 4.5 25.2 1.0 CG B:PRO25 4.7 26.3 1.0 CB B:ILE105 4.8 23.8 1.0 CB B:PRO25 4.9 24.4 1.0 N B:THR33 4.9 23.4 1.0

Fluorine binding site 7 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:26.8 occ:1.00 F18 B:K89201 0.0 26.8 1.0 C12 B:K89201 1.3 22.3 1.0 C11 B:K89201 2.4 19.2 1.0 C13 B:K89201 2.4 27.6 1.0 F17 B:K89201 2.8 27.7 1.0 OG1 B:THR33 3.1 24.9 1.0 CB C:ARG127 3.2 22.9 1.0 C10 B:K89201 3.6 22.9 1.0 C14 B:K89201 3.6 22.5 1.0 CD C:ARG127 3.8 22.6 1.0 O B:ASP29 3.8 21.2 1.0 CG B:PRO25 4.0 26.3 1.0 CB B:THR33 4.0 25.3 1.0 CB B:PRO25 4.1 24.4 1.0 C15 B:K89201 4.1 24.2 1.0 CG C:ARG127 4.1 23.3 1.0 O C:ARG127 4.2 26.5 1.0 C B:ASP29 4.3 26.6 1.0 C C:ARG127 4.3 25.9 1.0 O C:VAL124 4.4 24.8 1.0 CA C:ARG127 4.4 24.1 1.0 CB B:ASP29 4.4 24.7 1.0 CG2 B:THR33 4.5 23.5 1.0 F16 B:K89201 4.7 26.1 1.0 N B:LEU30 4.8 21.9 1.0 N09 B:K89201 4.8 22.8 1.0 CA C:VAL124 4.8 26.3 1.0 N C:THR128 4.8 24.2 1.0 CA B:LEU30 4.9 19.9 1.0 CD2 B:LEU30 4.9 28.4 1.0 CA B:ASP29 5.0 22.5 1.0 CG1 C:VAL124 5.0 27.7 1.0

Fluorine binding site 8 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:28.9 occ:1.00 F29 B:K89201 0.0 28.9 1.0 C03 B:K89201 1.3 25.3 1.0 C04 B:K89201 2.3 20.8 1.0 C02 B:K89201 2.3 23.5 1.0 O20 B:K89201 2.8 28.4 1.0 O B:HOH343 3.0 48.1 1.0 S19 B:K89201 3.1 25.1 1.0 CD1 B:ILE139 3.2 34.6 1.0 CD C:PRO134 3.3 47.5 1.0 CG C:PRO134 3.3 44.5 1.0 C23 B:K89201 3.4 36.5 1.0 N22 B:K89201 3.5 24.5 1.0 C05 B:K89201 3.5 19.9 1.0 C01 B:K89201 3.6 22.1 1.0 O C:ALA132 4.0 37.0 1.0 C06 B:K89201 4.1 19.5 1.0 O B:HOH320 4.3 34.7 1.0 O21 B:K89201 4.4 25.4 1.0 N B:LEU140 4.4 41.0 1.0 N C:PRO134 4.6 47.2 1.0 C27 B:K89201 4.7 31.1 1.0 CB B:LEU140 4.7 42.7 1.0 CG1 B:ILE139 4.7 48.0 1.0 CB C:PRO134 4.8 49.9 1.0 C24 B:K89201 4.8 36.1 1.0 O B:LEU140 4.9 49.6 1.0 O B:PRO138 4.9 31.6 1.0 CA B:ILE139 5.0 43.8 1.0

Fluorine binding site 9 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:28.8 occ:1.00 F16 C:K89201 0.0 28.8 1.0 C14 C:K89201 1.3 26.0 1.0 C15 C:K89201 2.3 25.4 1.0 C13 C:K89201 2.4 30.9 1.0 F17 C:K89201 2.8 28.6 1.0 CG2 C:ILE105 3.2 26.0 1.0 CB C:ILE105 3.5 24.3 1.0 OG C:SER106 3.6 23.6 0.6 C12 C:K89201 3.6 27.6 1.0 C10 C:K89201 3.6 25.4 1.0 CD1 C:TRP102 3.7 27.7 1.0 CD2 C:LEU30 3.8 30.0 1.0 O C:TRP102 4.1 24.1 1.0 C11 C:K89201 4.1 24.1 1.0 CA C:TRP102 4.2 21.3 1.0 N C:SER106 4.3 24.9 0.6 N C:SER106 4.3 24.6 0.4 NE1 C:TRP102 4.4 24.3 1.0 CD1 C:ILE105 4.4 24.8 1.0 CG C:TRP102 4.4 25.6 1.0 C C:ILE105 4.5 23.6 1.0 CG1 C:ILE105 4.5 25.2 1.0 CA C:ILE105 4.6 22.1 1.0 C C:TRP102 4.6 21.0 1.0 F18 C:K89201 4.7 32.9 1.0 N09 C:K89201 4.7 24.1 1.0 CB C:SER106 4.7 26.6 0.6 CB C:SER106 4.8 26.3 0.4 CB C:TRP102 4.8 20.0 1.0 CA C:SER106 4.8 25.3 0.6 CA C:SER106 4.8 25.3 0.4 O08 C:K89201 4.9 26.8 1.0 CG2 C:THR33 4.9 26.1 1.0 O C:LEU101 5.0 25.3 1.0

Fluorine binding site 10 out of 24 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Sulfamoylbenzamide (SBA_R01) within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:28.6 occ:1.00 F17 C:K89201 0.0 28.6 1.0 C13 C:K89201 1.3 30.9 1.0 C12 C:K89201 2.4 27.6 1.0 C14 C:K89201 2.4 26.0 1.0 F18 C:K89201 2.7 32.9 1.0 F16 C:K89201 2.8 28.8 1.0 CD2 C:LEU30 3.1 30.0 1.0 CB C:THR33 3.2 26.6 1.0 OG1 C:THR33 3.3 25.4 1.0 CG2 C:THR33 3.4 26.1 1.0 CA C:LEU30 3.6 22.5 1.0 C11 C:K89201 3.7 24.1 1.0 C15 C:K89201 3.7 25.4 1.0 CD1 C:ILE105 4.0 24.8 1.0 CG C:LEU30 4.0 24.9 1.0 O C:ASP29 4.1 25.7 1.0 O C:LEU30 4.1 25.3 1.0 CG2 C:ILE105 4.2 26.0 1.0 CB C:LEU30 4.2 19.9 1.0 C10 C:K89201 4.2 25.4 1.0 C C:LEU30 4.3 24.9 1.0 N C:LEU30 4.4 24.8 1.0 C C:ASP29 4.6 29.5 1.0 CA C:THR33 4.6 26.8 1.0 CB C:ILE105 4.7 24.3 1.0 CG C:PRO25 4.7 25.1 1.0 CG1 C:ILE105 4.9 25.2 1.0

Z.Zhou, T.Hu, X.Zhou, S.Wildum, F.Garcia-Alcalde, Z.H.Xu, D.Wu, Y.Mao, X.Tian, Y.Zhou, F.Shen, Z.Zhang, G.Tang, I.Najera, G.Yang, H.C.Shen, J.A.T.Young, N.Qin. Heteroaryldihydropyrimidine (Hap) and Sulfamoylbenzamide (Sba) Inhibit Hepatitis B Virus Replication By Different Molecular Mechanisms Sci Rep V. 7 42374 2017.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP42374