Chlorine 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:

Fluorine

(F)

14 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506, PDB code: 8gbu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl501 b:83.3 occ:0.40 CL30 A:YWE501 0.0 83.3 0.4 C26 A:YWE501 1.2 59.9 0.5 C27 A:YWE501 1.6 62.3 0.5 C29 A:YWE501 1.8 82.3 0.4 F28 A:YWE501 1.9 64.8 0.5 C25 A:YWE501 2.5 57.5 0.5 C31 A:YWE501 2.7 80.2 0.4 C27 A:YWE501 2.8 81.2 0.4 C29 A:YWE501 2.8 60.5 0.5 F28 A:YWE501 3.0 81.2 0.4 OG A:SER106 3.0 60.3 1.0 CG2 A:ILE105 3.4 62.3 1.0 C24 A:YWE501 3.4 59.9 0.5 CB A:ILE105 3.5 63.4 1.0 C31 A:YWE501 3.6 60.3 0.5 N A:SER106 3.7 65.2 1.0 CD1 A:TRP102 3.7 60.2 1.0 O A:TRP102 3.7 52.0 1.0 CD2 A:LEU30 3.8 67.3 1.0 C24 A:YWE501 4.0 80.9 0.4 CA A:TRP102 4.0 54.7 1.0 C26 A:YWE501 4.0 79.8 0.4 CL30 A:YWE501 4.1 55.5 0.5 CB A:SER106 4.2 60.2 1.0 CA A:SER106 4.2 61.2 1.0 C A:ILE105 4.2 66.5 1.0 NE1 A:TRP102 4.3 60.7 1.0 C A:TRP102 4.3 56.7 1.0 CG A:TRP102 4.3 59.6 1.0 CA A:ILE105 4.4 66.6 1.0 CD1 A:ILE105 4.4 57.9 1.0 C25 A:YWE501 4.5 80.3 0.4 CG1 A:ILE105 4.5 59.9 1.0 CB A:TRP102 4.7 57.1 1.0 N23 A:YWE501 4.7 61.1 0.5 O A:LEU101 4.8 58.5 1.0 O22 A:YWE501 4.9 72.8 0.4 N A:ILE105 5.0 66.9 1.0

Chlorine binding site 2 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl501 b:55.5 occ:0.50 CL30 A:YWE501 0.0 55.5 0.5 C26 A:YWE501 1.4 79.8 0.4 F28 A:YWE501 1.5 81.2 0.4 C27 A:YWE501 1.5 81.2 0.4 C29 A:YWE501 1.8 60.5 0.5 C27 A:YWE501 2.7 62.3 0.5 C31 A:YWE501 2.8 60.3 0.5 C25 A:YWE501 2.8 80.3 0.4 F28 A:YWE501 2.9 64.8 0.5 C29 A:YWE501 2.9 82.3 0.4 OG1 A:THR33 3.3 43.5 1.0 C24 A:YWE501 3.7 80.9 0.4 C31 A:YWE501 3.8 80.2 0.4 CG A:PRO25 3.8 59.4 1.0 CB A:PRO25 3.9 58.8 1.0 C26 A:YWE501 4.0 59.9 0.5 C24 A:YWE501 4.0 59.9 0.5 CD2 A:LEU30 4.1 67.3 1.0 CB A:THR33 4.1 50.2 1.0 O A:ASP29 4.1 54.7 1.0 CL30 A:YWE501 4.1 83.3 0.4 CG2 A:THR33 4.2 48.4 1.0 C A:ASP29 4.5 62.1 1.0 CA A:LEU30 4.5 70.0 1.0 C25 A:YWE501 4.5 57.5 0.5 CG A:LEU30 4.6 68.8 1.0 N A:LEU30 4.7 68.0 1.0 CB A:ASP29 4.9 70.0 1.0

Chlorine binding site 3 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl502 b:92.9 occ:0.91 CL30 A:YWE502 0.0 92.9 0.9 C29 A:YWE502 1.8 78.2 0.9 C31 A:YWE502 2.6 72.8 0.9 C27 A:YWE502 2.8 74.8 0.9 F28 A:YWE502 3.1 71.1 0.9 CG2 F:ILE105 3.3 63.4 1.0 CB F:ILE105 3.5 60.9 1.0 OG F:SER106 3.5 59.5 1.0 N F:SER106 3.8 63.0 1.0 CD2 F:LEU30 3.9 70.0 1.0 C24 A:YWE502 3.9 77.1 0.9 C26 A:YWE502 4.0 74.8 0.9 CD1 F:TRP102 4.2 61.0 1.0 CD1 F:ILE105 4.2 59.9 1.0 C F:ILE105 4.3 64.1 1.0 O F:TRP102 4.3 59.2 1.0 CA F:SER106 4.4 61.8 1.0 C25 A:YWE502 4.5 77.4 0.9 CG1 F:ILE105 4.5 60.5 1.0 CA F:ILE105 4.5 64.6 1.0 CA F:TRP102 4.6 62.7 1.0 CB F:SER106 4.6 60.4 1.0 CG2 F:THR33 4.6 51.1 1.0 NE1 F:TRP102 4.7 63.0 1.0 CG F:TRP102 4.9 64.0 1.0 C F:TRP102 4.9 60.5 1.0

Chlorine binding site 4 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 B:Cl501 b:77.9 occ:0.92 CL30 B:YWE501 0.0 77.9 0.9 C29 B:YWE501 1.8 61.1 0.9 C27 B:YWE501 2.6 63.7 0.9 C31 B:YWE501 2.7 56.5 0.9 F28 B:YWE501 2.8 67.8 0.9 OG1 B:THR33 3.1 48.1 1.0 CG B:PRO25 3.6 68.5 1.0 O B:ASP29 3.7 54.8 1.0 CB B:PRO25 3.8 66.1 1.0 CB B:THR33 3.9 53.7 1.0 C26 B:YWE501 3.9 62.2 0.9 C24 B:YWE501 3.9 59.0 0.9 CB C:ARG127 4.1 61.3 1.0 CD2 B:LEU30 4.1 70.1 1.0 CG2 B:THR33 4.2 53.1 1.0 C B:ASP29 4.3 63.6 1.0 CA B:LEU30 4.3 71.2 1.0 C25 B:YWE501 4.4 62.3 0.9 CD C:ARG127 4.4 62.5 1.0 N B:LEU30 4.6 68.9 1.0 CG B:LEU30 4.7 70.0 1.0 O C:ARG127 4.9 63.0 1.0 O C:VAL124 4.9 52.0 1.0 C C:ARG127 5.0 58.7 1.0 CG C:ARG127 5.0 61.5 1.0 CB B:ASP29 5.0 66.3 1.0 CD B:PRO25 5.0 68.6 1.0

Chlorine binding site 5 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 C:Cl501 b:89.7 occ:0.94 CL30 C:YWE501 0.0 89.7 0.9 C29 C:YWE501 1.8 76.2 0.9 C27 C:YWE501 2.7 74.5 0.9 C31 C:YWE501 2.7 73.1 0.9 F28 C:YWE501 2.9 81.0 0.9 OG1 C:THR33 3.1 47.4 1.0 O C:ASP29 3.7 54.8 1.0 CG C:PRO25 3.7 67.4 1.0 CD2 C:LEU30 3.9 64.2 1.0 CB C:PRO25 3.9 67.8 1.0 CB C:THR33 3.9 52.4 1.0 C26 C:YWE501 4.0 69.1 0.9 C24 C:YWE501 4.0 74.2 0.9 CA C:LEU30 4.0 68.7 1.0 C C:ASP29 4.1 65.2 1.0 N C:LEU30 4.3 70.1 1.0 CG2 C:THR33 4.3 49.0 1.0 CG C:LEU30 4.4 65.8 1.0 C25 C:YWE501 4.4 72.1 0.9 CB C:ASP29 4.7 71.8 1.0 CB C:LEU30 4.8 66.7 1.0

Chlorine binding site 6 out of 7 in the Hepatitis B Capsid Y132A Mutant with Compound Ab-506


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 E:Cl501 b:83.4 occ:0.95 CL30 E:YWE501 0.0 83.4 0.9 C29 E:YWE501 1.8 73.8 0.9 C31 E:YWE501 2.7 74.5 0.9 C27 E:YWE501 2.7 75.1 0.9 F28 E:YWE501 2.9 83.3 0.9 OG1 D:THR33 3.3 40.3 1.0 O D:ASP29 3.7 62.8 1.0 CD2 D:LEU30 3.8 67.0 1.0 CB D:THR33 3.9 47.8 1.0 C24 E:YWE501 3.9 75.8 0.9 CG D:PRO25 3.9 64.8 1.0 C26 E:YWE501 4.0 73.3 0.9 CB D:PRO25 4.0 64.7 1.0 C D:ASP29 4.0 61.9 1.0 CA D:LEU30 4.1 66.4 1.0 CB E:ARG127 4.1 58.6 1.0 N D:LEU30 4.2 67.5 1.0 CG2 D:THR33 4.2 47.1 1.0 CD E:ARG127 4.3 56.4 1.0 CG D:LEU30 4.4 64.8 1.0 C25 E:YWE501 4.4 74.8 0.9 CB D:ASP29 4.6 54.6 1.0 CB D:LEU30 4.8 65.7 1.0 CG E:ARG127 4.9 58.0 1.0 O E:VAL124 4.9 57.3 1.0 O E:ARG127 4.9 61.5 1.0 CA D:ASP29 5.0 55.9 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 E:Cl502 b:71.2 occ:0.91 CL30 E:YWE502 0.0 71.2 0.9 C29 E:YWE502 1.8 63.1 0.9 C27 E:YWE502 2.7 61.3 0.9 C31 E:YWE502 2.7 61.6 0.9 F28 E:YWE502 2.8 68.0 0.9 OG1 E:THR33 3.1 44.8 1.0 O E:ASP29 3.8 51.4 1.0 CG E:PRO25 3.8 59.1 1.0 CB E:THR33 3.8 52.4 1.0 CD2 E:LEU30 3.9 65.0 1.0 CB E:PRO25 3.9 58.3 1.0 C26 E:YWE502 4.0 57.0 0.9 C24 E:YWE502 4.0 63.0 0.9 CG2 E:THR33 4.2 50.9 1.0 C E:ASP29 4.2 63.3 1.0 CA E:LEU30 4.2 66.1 1.0 N E:LEU30 4.4 68.9 1.0 C25 E:YWE502 4.4 60.6 0.9 CG E:LEU30 4.5 66.9 1.0 CB E:ASP29 4.8 68.4 1.0 CB E:LEU30 4.9 65.4 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