Fluorine in PDB 8gbu: Hepatitis B Capsid Y132A Mutant with Compound Ab-506

The structure of Hepatitis B Capsid Y132A Mutant with Compound Ab-506, PDB code: 8gbu was solved by P.S.Horanyi, S.J.Mayclin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.78 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.936, 87.879, 100.827, 90, 104.12, 90
R / Rfree (%)	23.3 / 28.5

The structure of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506 (pdb code 8gbu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506, PDB code: 8gbu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:96.0 occ:0.40 F19 A:YWE501 0.0 96.0 0.4 F19 A:YWE501 0.3 63.8 0.5 C18 A:YWE501 1.4 93.4 0.4 C18 A:YWE501 1.4 64.1 0.5 C17 A:YWE501 2.3 63.9 0.5 C17 A:YWE501 2.3 92.0 0.4 C20 A:YWE501 2.4 92.8 0.4 C20 A:YWE501 2.4 63.6 0.5 N10 A:YWE501 3.0 93.4 0.4 C11 A:YWE501 3.0 92.8 0.4 N10 A:YWE501 3.1 61.4 0.5 C11 A:YWE501 3.2 62.3 0.5 N A:LEU140 3.5 85.9 1.0 C16 A:YWE501 3.6 63.9 0.5 C16 A:YWE501 3.6 90.5 0.4 C14 A:YWE501 3.6 90.0 0.4 C14 A:YWE501 3.7 62.2 0.5 C08 A:YWE501 3.7 62.3 0.5 CA A:ILE139 3.8 87.9 1.0 C08 A:YWE501 3.9 95.6 0.4 CB A:ILE139 4.1 97.5 1.0 C15 A:YWE501 4.1 86.8 0.4 C15 A:YWE501 4.1 61.9 0.5 C A:ILE139 4.2 86.0 1.0 O07 A:YWE501 4.2 70.8 0.5 CG2 A:ILE139 4.2 93.5 1.0 O09 A:YWE501 4.3 55.6 0.5 O A:LEU140 4.3 93.3 1.0 CB A:LEU140 4.3 83.5 1.0 O A:PRO138 4.3 73.5 1.0 O09 A:YWE501 4.3 88.5 0.4 C12 A:YWE501 4.4 92.5 0.4 CA A:LEU140 4.4 87.1 1.0 C12 A:YWE501 4.5 62.8 0.5 C13 A:YWE501 4.7 90.4 0.4 O07 A:YWE501 4.8 102.2 0.4 C13 A:YWE501 4.8 61.6 0.5 C A:LEU140 4.9 93.2 1.0 N A:ILE139 4.9 84.3 1.0

Fluorine binding site 2 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:63.8 occ:0.50 F19 A:YWE501 0.0 63.8 0.5 F19 A:YWE501 0.3 96.0 0.4 C18 A:YWE501 1.4 64.1 0.5 C18 A:YWE501 1.4 93.4 0.4 C20 A:YWE501 2.3 92.8 0.4 C17 A:YWE501 2.3 63.9 0.5 C20 A:YWE501 2.4 63.6 0.5 C17 A:YWE501 2.4 92.0 0.4 N10 A:YWE501 2.8 93.4 0.4 C11 A:YWE501 2.9 92.8 0.4 N10 A:YWE501 3.0 61.4 0.5 C11 A:YWE501 3.1 62.3 0.5 N A:LEU140 3.3 85.9 1.0 C14 A:YWE501 3.6 90.0 0.4 C16 A:YWE501 3.6 63.9 0.5 C08 A:YWE501 3.6 62.3 0.5 C16 A:YWE501 3.6 90.5 0.4 C14 A:YWE501 3.6 62.2 0.5 CA A:ILE139 3.7 87.9 1.0 C08 A:YWE501 3.8 95.6 0.4 CB A:ILE139 4.0 97.5 1.0 C A:ILE139 4.0 86.0 1.0 O07 A:YWE501 4.0 70.8 0.5 O A:LEU140 4.1 93.3 1.0 C15 A:YWE501 4.1 86.8 0.4 CB A:LEU140 4.1 83.5 1.0 C15 A:YWE501 4.1 61.9 0.5 CG2 A:ILE139 4.1 93.5 1.0 CA A:LEU140 4.2 87.1 1.0 O09 A:YWE501 4.3 88.5 0.4 O09 A:YWE501 4.3 55.6 0.5 C12 A:YWE501 4.3 92.5 0.4 O A:PRO138 4.4 73.5 1.0 C12 A:YWE501 4.4 62.8 0.5 O07 A:YWE501 4.6 102.2 0.4 C A:LEU140 4.6 93.2 1.0 C13 A:YWE501 4.7 90.4 0.4 C13 A:YWE501 4.8 61.6 0.5 N A:ILE139 4.9 84.3 1.0

Fluorine binding site 3 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:81.2 occ:0.40 F28 A:YWE501 0.0 81.2 0.4 C27 A:YWE501 1.3 81.2 0.4 CL30 A:YWE501 1.5 55.5 0.5 F28 A:YWE501 1.5 64.8 0.5 C29 A:YWE501 1.8 60.5 0.5 C27 A:YWE501 1.9 62.3 0.5 C26 A:YWE501 2.3 79.8 0.4 C29 A:YWE501 2.4 82.3 0.4 CD2 A:LEU30 3.0 67.3 1.0 CL30 A:YWE501 3.0 83.3 0.4 C31 A:YWE501 3.2 60.3 0.5 C26 A:YWE501 3.2 59.9 0.5 OG1 A:THR33 3.5 43.5 1.0 C25 A:YWE501 3.6 80.3 0.4 C31 A:YWE501 3.6 80.2 0.4 CB A:THR33 3.8 50.2 1.0 CA A:LEU30 3.9 70.0 1.0 CG A:LEU30 3.9 68.8 1.0 CG2 A:THR33 3.9 48.4 1.0 CG A:PRO25 4.0 59.4 1.0 C24 A:YWE501 4.1 80.9 0.4 C24 A:YWE501 4.1 59.9 0.5 C25 A:YWE501 4.1 57.5 0.5 CB A:PRO25 4.3 58.8 1.0 O A:ASP29 4.3 54.7 1.0 CB A:LEU30 4.4 68.6 1.0 N A:LEU30 4.5 68.0 1.0 CD1 A:ILE105 4.6 57.9 1.0 CG2 A:ILE105 4.6 62.3 1.0 O A:LEU30 4.6 68.7 1.0 C A:ASP29 4.7 62.1 1.0 C A:LEU30 4.8 68.2 1.0

Fluorine binding site 4 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:64.8 occ:0.50 F28 A:YWE501 0.0 64.8 0.5 C27 A:YWE501 1.4 62.3 0.5 F28 A:YWE501 1.5 81.2 0.4 CL30 A:YWE501 1.9 83.3 0.4 C27 A:YWE501 2.1 81.2 0.4 C29 A:YWE501 2.2 82.3 0.4 C29 A:YWE501 2.4 60.5 0.5 C26 A:YWE501 2.4 59.9 0.5 CL30 A:YWE501 2.9 55.5 0.5 CG2 A:ILE105 3.2 62.3 1.0 CD2 A:LEU30 3.3 67.3 1.0 C26 A:YWE501 3.4 79.8 0.4 C31 A:YWE501 3.5 80.2 0.4 CB A:ILE105 3.6 63.4 1.0 C25 A:YWE501 3.6 57.5 0.5 C31 A:YWE501 3.6 60.3 0.5 CD1 A:ILE105 3.7 57.9 1.0 CG2 A:THR33 3.7 48.4 1.0 CB A:THR33 3.9 50.2 1.0 C24 A:YWE501 4.1 59.9 0.5 CG1 A:ILE105 4.2 59.9 1.0 OG1 A:THR33 4.2 43.5 1.0 C25 A:YWE501 4.4 80.3 0.4 C24 A:YWE501 4.4 80.9 0.4 CG A:LEU30 4.5 68.8 1.0 CA A:LEU30 4.6 70.0 1.0 O A:LEU30 4.7 68.7 1.0 CB A:LEU30 4.9 68.6 1.0 OG A:SER106 4.9 60.3 1.0 CA A:ILE105 5.0 66.6 1.0

Fluorine binding site 5 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:65.7 occ:0.91 F19 A:YWE502 0.0 65.7 0.9 C18 A:YWE502 1.3 70.2 0.9 C17 A:YWE502 2.3 71.5 0.9 C20 A:YWE502 2.3 73.6 0.9 N10 A:YWE502 2.8 73.1 0.9 C11 A:YWE502 3.0 74.5 0.9 CD A:PRO134 3.1 69.7 1.0 CG A:PRO134 3.2 69.8 1.0 N F:LEU140 3.6 94.5 1.0 C16 A:YWE502 3.6 72.1 0.9 C14 A:YWE502 3.6 72.4 0.9 C08 A:YWE502 3.7 71.9 0.9 CA F:ILE139 3.8 88.3 1.0 O A:ALA132 3.9 72.1 1.0 CB F:ILE139 4.0 89.3 1.0 CG2 F:ILE139 4.0 83.2 1.0 C15 A:YWE502 4.1 71.7 0.9 O F:LEU140 4.2 93.5 1.0 C F:ILE139 4.3 91.3 1.0 C12 A:YWE502 4.3 76.7 0.9 O09 A:YWE502 4.3 61.5 0.9 O07 A:YWE502 4.4 79.3 0.9 O F:PRO138 4.4 78.9 1.0 N A:PRO134 4.5 71.3 1.0 CA F:LEU140 4.6 92.3 1.0 CB F:LEU140 4.6 91.2 1.0 C13 A:YWE502 4.7 73.8 0.9 CB A:PRO134 4.7 70.6 1.0 C F:LEU140 4.8 91.3 1.0 CE1 F:TYR118 5.0 63.6 1.0 N F:ILE139 5.0 86.0 1.0

Fluorine binding site 6 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:71.1 occ:0.91 F28 A:YWE502 0.0 71.1 0.9 C27 A:YWE502 1.3 74.8 0.9 C26 A:YWE502 2.3 74.8 0.9 C29 A:YWE502 2.4 78.2 0.9 OG1 F:THR33 3.1 43.4 1.0 CL30 A:YWE502 3.1 92.9 0.9 CB F:THR33 3.4 49.9 1.0 CD2 F:LEU30 3.4 70.0 1.0 C25 A:YWE502 3.6 77.4 0.9 O F:ASP29 3.6 63.5 1.0 CG2 F:THR33 3.7 51.1 1.0 C31 A:YWE502 3.7 72.8 0.9 CA F:LEU30 3.8 71.5 1.0 CG F:PRO25 4.0 64.9 1.0 CG F:LEU30 4.1 71.0 1.0 C24 A:YWE502 4.1 77.1 0.9 C F:ASP29 4.2 66.1 1.0 N F:LEU30 4.3 70.2 1.0 CB F:PRO25 4.4 63.9 1.0 CB F:LEU30 4.5 71.6 1.0 O F:LEU30 4.7 65.4 1.0 C F:LEU30 4.7 66.8 1.0 CD1 F:ILE105 4.9 59.9 1.0 CA F:THR33 4.9 54.6 1.0

Fluorine binding site 7 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:63.0 occ:0.92 F19 B:YWE501 0.0 63.0 0.9 C18 B:YWE501 1.3 59.6 0.9 C17 B:YWE501 2.3 58.3 0.9 C20 B:YWE501 2.4 59.9 0.9 N10 B:YWE501 2.9 64.2 0.9 C11 B:YWE501 3.0 59.1 0.9 CD C:PRO134 3.2 59.8 1.0 CG C:PRO134 3.2 60.6 1.0 N B:LEU140 3.2 77.2 1.0 C16 B:YWE501 3.6 60.0 0.9 C14 B:YWE501 3.7 59.0 0.9 C08 B:YWE501 3.7 67.5 0.9 CA B:ILE139 3.8 77.8 1.0 O C:ALA132 4.0 71.2 1.0 O B:LEU140 4.0 87.2 1.0 C B:ILE139 4.0 77.0 1.0 CG2 B:ILE139 4.1 86.6 1.0 CB B:LEU140 4.1 71.8 1.0 O09 B:YWE501 4.1 67.0 0.9 C15 B:YWE501 4.2 59.8 0.9 CA B:LEU140 4.2 75.5 1.0 O B:PRO138 4.3 62.9 1.0 C12 B:YWE501 4.4 58.2 0.9 CD1 B:ILE139 4.5 84.2 1.0 N C:PRO134 4.5 60.9 1.0 CB B:ILE139 4.5 84.0 1.0 C B:LEU140 4.5 83.8 1.0 O07 B:YWE501 4.6 68.1 0.9 CB C:PRO134 4.7 63.2 1.0 C13 B:YWE501 4.7 57.5 0.9 CE2 B:TYR118 4.8 63.2 1.0 N B:ILE139 4.9 75.0 1.0

Fluorine binding site 8 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:67.8 occ:0.92 F28 B:YWE501 0.0 67.8 0.9 C27 B:YWE501 1.3 63.7 0.9 C26 B:YWE501 2.3 62.2 0.9 C29 B:YWE501 2.4 61.1 0.9 CL30 B:YWE501 2.8 77.9 0.9 CG2 B:ILE105 3.1 66.6 1.0 CD2 B:LEU30 3.3 70.1 1.0 C25 B:YWE501 3.5 62.3 0.9 C31 B:YWE501 3.6 56.5 0.9 CB B:ILE105 3.7 61.3 1.0 CD1 B:ILE105 3.7 60.8 1.0 CG2 B:THR33 3.9 53.1 1.0 CB B:THR33 4.0 53.7 1.0 C24 B:YWE501 4.1 59.0 0.9 OG1 B:THR33 4.2 48.1 1.0 CG1 B:ILE105 4.2 61.1 1.0 CG B:LEU30 4.6 70.0 1.0 CA B:LEU30 4.6 71.2 1.0 O B:LEU30 4.7 68.8 1.0 CG B:PRO25 4.8 68.5 1.0 CD1 B:TRP102 4.9 56.9 1.0 CA B:TRP102 4.9 57.9 1.0 CB B:LEU30 4.9 71.3 1.0

Fluorine binding site 9 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:104.7 occ:0.94 F19 C:YWE501 0.0 104.7 0.9 C18 C:YWE501 1.3 93.8 0.9 C20 C:YWE501 2.3 95.6 0.9 C17 C:YWE501 2.4 93.7 0.9 N10 C:YWE501 2.9 90.2 0.9 C11 C:YWE501 3.0 93.4 0.9 C16 C:YWE501 3.6 88.7 0.9 C14 C:YWE501 3.6 94.5 0.9 C08 C:YWE501 3.7 88.3 0.9 N C:LEU140 3.7 87.1 1.0 CG2 C:ILE139 3.8 82.9 1.0 CA C:ILE139 4.0 80.7 1.0 O C:LEU140 4.0 88.5 1.0 CB C:ILE139 4.0 87.4 1.0 O09 C:YWE501 4.1 87.4 0.9 C15 C:YWE501 4.2 87.1 0.9 C12 C:YWE501 4.3 95.7 0.9 C C:ILE139 4.4 83.2 1.0 O07 C:YWE501 4.6 91.9 0.9 CA C:LEU140 4.6 89.4 1.0 O C:PRO138 4.6 70.3 1.0 CB C:LEU140 4.6 87.0 1.0 C13 C:YWE501 4.7 93.8 0.9 C C:LEU140 4.8 92.9 1.0

Fluorine binding site 10 out of 14 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hepatitis B Capsid Y132A Mutant with Compound Ab-506 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:81.0 occ:0.94 F28 C:YWE501 0.0 81.0 0.9 C27 C:YWE501 1.3 74.5 0.9 C26 C:YWE501 2.3 69.1 0.9 C29 C:YWE501 2.4 76.2 0.9 CL30 C:YWE501 2.9 89.7 0.9 CG2 C:ILE105 3.1 66.3 1.0 CD2 C:LEU30 3.3 64.2 1.0 CD1 C:ILE105 3.5 54.1 1.0 C25 C:YWE501 3.5 72.1 0.9 CB C:ILE105 3.6 62.7 1.0 C31 C:YWE501 3.6 73.1 0.9 CG2 C:THR33 4.0 49.0 1.0 CG1 C:ILE105 4.0 58.6 1.0 CB C:THR33 4.1 52.4 1.0 C24 C:YWE501 4.1 74.2 0.9 OG1 C:THR33 4.4 47.4 1.0 CA C:LEU30 4.5 68.7 1.0 CG C:LEU30 4.5 65.8 1.0 O C:LEU30 4.6 73.9 1.0 CB C:LEU30 4.8 66.7 1.0 CD1 C:TRP102 4.8 59.6 1.0 CA C:TRP102 5.0 60.5 1.0 CA C:ILE105 5.0 65.6 1.0

A.G.Cole, S.G.Kultgen, N.Mani, J.G.Quintero, K.Yi Fan, A.Ardzinski, K.Stever, B.D.Dorsey, J.R.Phelps, A.C.H.Lee, E.P.Thi, T.Chiu, S.Tang, P.S.Horanyi, S.J.Mayclin, T.O.Harasym, M.J.Sofia. Design, Synthesis, and Structure-Activity Relationship of A Bicyclic Hbv Capsid Assembly Modulator Chemotype Leading to the Identification of Clinical Candidate Ab-506. Bioorg.Med.Chem.Lett. 29456 2023.
ISSN: ESSN 1464-3405
PubMed: 37633618
DOI: 10.1016/J.BMCL.2023.129456