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

Protein crystallography data

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

Other elements in 8gbu:

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

Fluorine (F) 14 atoms

Chlorine Binding Sites:

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 8gbu

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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 8gbu

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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 8gbu

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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 8gbu

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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 8gbu

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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 8gbu

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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 8gbu

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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

Reference:

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
Page generated: Thu Dec 28 03:14:06 2023

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