Fluorine in PDB 8i71: Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam), PDB code: 8i71 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)	33.51 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.392, 67.565, 86.246, 68.6, 69.81, 83.87
R / Rfree (%)	15.5 / 19.3

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Fluorine atom in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) (pdb code 8i71). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam), PDB code: 8i71:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ A:F206 b:30.2 occ:1.00 F37 A:OTI206 0.0 30.2 1.0 C34 A:OTI206 1.4 28.7 1.0 C33 A:OTI206 2.3 27.6 1.0 C35 A:OTI206 2.4 26.9 1.0 C36 A:OTI206 2.8 27.0 1.0 CD2 A:LEU30 3.2 26.3 1.0 CB A:THR33 3.2 30.1 1.0 CG2 A:THR33 3.3 30.6 1.0 OG1 A:THR33 3.4 28.9 1.0 C32 A:OTI206 3.6 27.6 1.0 C30 A:OTI206 3.7 26.9 1.0 CA A:LEU30 3.8 27.7 1.0 C31 A:OTI206 4.1 27.2 1.0 CD1 A:ILE105 4.2 25.2 1.0 CG2 A:ILE105 4.2 27.8 1.0 CG A:LEU30 4.3 25.3 1.0 O A:ASP29 4.3 30.4 1.0 O A:LEU30 4.3 30.3 1.0 CB A:LEU30 4.4 25.3 1.0 C A:LEU30 4.6 29.7 1.0 N A:LEU30 4.6 27.8 1.0 CA A:THR33 4.7 29.6 1.0 CB A:ILE105 4.7 25.7 1.0 C42 A:OTI206 4.7 30.3 1.0 CG A:PRO25 4.8 26.6 1.0 C A:ASP29 4.8 29.4 1.0 C21 A:OTI206 4.9 27.6 1.0

Fluorine binding site 2 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ B:F204 b:29.2 occ:1.00 F37 B:OTI204 0.0 29.2 1.0 C34 B:OTI204 1.4 26.2 1.0 C33 B:OTI204 2.3 26.1 1.0 C35 B:OTI204 2.4 24.8 1.0 C36 B:OTI204 2.8 25.4 1.0 CD2 B:LEU30 3.2 24.5 1.0 CB B:THR33 3.3 27.3 1.0 CG2 B:THR33 3.4 27.7 1.0 OG1 B:THR33 3.5 27.7 1.0 C32 B:OTI204 3.6 24.8 1.0 C30 B:OTI204 3.6 25.1 1.0 CA B:LEU30 3.8 23.8 1.0 C31 B:OTI204 4.1 24.7 1.0 O B:ASP29 4.2 27.5 1.0 CD1 B:ILE105 4.2 21.9 1.0 CG2 B:ILE105 4.2 26.5 1.0 CG B:LEU30 4.3 23.5 1.0 O B:LEU30 4.4 26.9 1.0 CB B:LEU30 4.5 22.9 1.0 N B:LEU30 4.6 24.8 1.0 C B:LEU30 4.6 24.8 1.0 C42 B:OTI204 4.6 34.4 1.0 CG B:PRO25 4.7 25.7 1.0 C B:ASP29 4.7 26.5 1.0 CA B:THR33 4.7 28.2 1.0 CB B:ILE105 4.8 24.8 1.0 C21 B:OTI204 4.9 25.7 1.0 CB B:PRO25 5.0 26.9 1.0

Fluorine binding site 3 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ C:F205 b:27.5 occ:1.00 F37 C:OTI205 0.0 27.5 1.0 C34 C:OTI205 1.4 26.2 1.0 C33 C:OTI205 2.3 25.6 1.0 C35 C:OTI205 2.4 23.9 1.0 C36 C:OTI205 2.8 22.9 1.0 CD2 C:LEU30 3.2 24.0 1.0 CB C:THR33 3.3 25.1 1.0 CG2 C:THR33 3.3 25.2 1.0 OG1 C:THR33 3.4 25.3 1.0 C32 C:OTI205 3.6 25.6 1.0 C30 C:OTI205 3.6 24.4 1.0 CA C:LEU30 3.8 21.7 1.0 C31 C:OTI205 4.1 24.3 1.0 CD1 C:ILE105 4.2 24.7 1.0 CG2 C:ILE105 4.2 25.8 1.0 O C:ASP29 4.2 25.3 1.0 CG C:LEU30 4.2 21.8 1.0 O C:LEU30 4.2 24.6 1.0 CB C:LEU30 4.4 20.9 1.0 C C:LEU30 4.5 24.2 1.0 C42 C:OTI205 4.5 29.6 1.0 N C:LEU30 4.6 24.0 1.0 CA C:THR33 4.7 25.6 1.0 CB C:ILE105 4.7 23.9 1.0 C C:ASP29 4.7 24.4 1.0 CG C:PRO25 4.8 24.6 1.0 C21 C:OTI205 4.9 25.4 1.0

Fluorine binding site 4 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ D:F204 b:28.6 occ:1.00 F37 D:OTI204 0.0 28.6 1.0 C34 D:OTI204 1.4 26.6 1.0 C33 D:OTI204 2.3 27.6 1.0 C35 D:OTI204 2.4 25.0 1.0 C36 D:OTI204 2.8 25.6 1.0 CD2 D:LEU30 3.2 26.0 1.0 CB D:THR33 3.2 27.8 1.0 CG2 D:THR33 3.3 27.1 1.0 OG1 D:THR33 3.4 27.7 1.0 C32 D:OTI204 3.6 26.3 1.0 C30 D:OTI204 3.6 25.0 1.0 CA D:LEU30 3.7 24.5 1.0 C31 D:OTI204 4.0 26.9 1.0 CG D:LEU30 4.2 24.1 1.0 O D:LEU30 4.2 28.1 1.0 O D:ASP29 4.2 26.0 1.0 CG2 D:ILE105 4.2 26.8 1.0 CD1 D:ILE105 4.3 25.7 1.0 CB D:LEU30 4.3 23.8 1.0 C D:LEU30 4.5 27.1 1.0 N D:LEU30 4.5 25.1 1.0 C42 D:OTI204 4.6 35.4 1.0 CA D:THR33 4.7 27.2 1.0 C D:ASP29 4.7 25.9 1.0 CG D:PRO25 4.8 26.0 1.0 CB D:ILE105 4.8 25.6 1.0 C21 D:OTI204 5.0 26.2 1.0

Fluorine binding site 5 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ E:F202 b:32.5 occ:1.00 F37 E:OTI202 0.0 32.5 1.0 C34 E:OTI202 1.4 32.2 1.0 C33 E:OTI202 2.3 31.0 1.0 C35 E:OTI202 2.4 30.0 1.0 C36 E:OTI202 2.8 30.2 1.0 CB E:THR33 3.2 31.4 1.0 CD2 E:LEU30 3.2 29.1 1.0 CG2 E:THR33 3.3 32.2 1.0 OG1 E:THR33 3.4 32.5 1.0 C32 E:OTI202 3.6 31.4 1.0 C30 E:OTI202 3.6 30.6 1.0 CA E:LEU30 3.9 28.3 1.0 C31 E:OTI202 4.0 30.5 1.0 CD1 E:ILE105 4.2 24.9 1.0 CG2 E:ILE105 4.2 26.7 1.0 O E:ASP29 4.2 29.5 1.0 CG E:LEU30 4.3 28.1 1.0 O E:LEU30 4.4 29.9 1.0 CB E:LEU30 4.5 26.4 1.0 N E:LEU30 4.6 29.3 1.0 CA E:THR33 4.7 31.5 1.0 C E:LEU30 4.7 29.5 1.0 C42 E:OTI202 4.7 35.3 1.0 CB E:ILE105 4.7 26.7 1.0 CG E:PRO25 4.8 27.3 1.0 C E:ASP29 4.8 30.5 1.0 C21 E:OTI202 4.9 30.1 1.0

Fluorine binding site 6 out of 6 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam)


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 Linvencorvir (RG7907), A Hepatitis B Virus (Hbv) Core Protein Allosteric Modulator (Cpam) within 5.0Å range: probe atom residue distance (Å) B Occ F:F203 b:28.5 occ:1.00 F37 F:OTI203 0.0 28.5 1.0 C34 F:OTI203 1.4 26.6 1.0 C33 F:OTI203 2.3 26.5 1.0 C35 F:OTI203 2.4 25.7 1.0 C36 F:OTI203 2.8 26.8 1.0 CD2 F:LEU30 3.2 25.8 1.0 CB F:THR33 3.2 29.0 1.0 CG2 F:THR33 3.4 28.3 1.0 OG1 F:THR33 3.4 30.2 1.0 C32 F:OTI203 3.6 26.8 1.0 C30 F:OTI203 3.6 26.0 1.0 CA F:LEU30 3.8 27.0 1.0 C31 F:OTI203 4.1 25.8 1.0 O F:ASP29 4.2 29.4 1.0 CG2 F:ILE105 4.2 27.2 1.0 CG F:LEU30 4.3 25.3 1.0 CD1 F:ILE105 4.3 26.2 1.0 O F:LEU30 4.4 28.4 1.0 CB F:LEU30 4.4 26.3 1.0 N F:LEU30 4.5 27.6 1.0 C F:LEU30 4.6 27.6 1.0 CA F:THR33 4.7 29.0 1.0 C F:ASP29 4.7 28.7 1.0 CG F:PRO25 4.7 24.2 1.0 C42 F:OTI203 4.8 30.2 1.0 CB F:ILE105 4.8 25.6 1.0 C21 F:OTI203 4.9 25.9 1.0

W.Zhang, L.Guo, H.Liu, G.Wu, H.Shi, M.Zhou, Z.Zhang, B.Kou, T.Hu, Z.Zhou, Z.Xu, X.Zhou, Y.Zhou, X.Tian, G.Yang, J.A.T.Young, H.Qiu, G.Ottaviani, J.Xie, A.V.Mayweg, H.C.Shen, W.Zhu. Discovery of Linvencorvir (RG7907), A Hepatitis B Virus Core Protein Allosteric Modulator, For the Treatment of Chronic Hbv Infection. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36896968
DOI: 10.1021/ACS.JMEDCHEM.3C00173