SMTL ID : 8gih.1

Structure of Hepatitis B Virus Capsid Y132A mutant in complex with Compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: R.42, D.43 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: P.138, A.140 Chain C: R.136 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain B: R.42, D.43 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: P.138, N.139, A.140 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain C: L.40, Y.41, R.42, D.43 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: P.138, A.140 Chain D: R.136 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: R.42, D.43 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain D: A.140 Chain E: R.136 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain E: R.42, D.43 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain E: A.140 Chain F: R.136 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain F: R.42, D.43 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: R.136 Chain F: P.138, A.140 Ligand excluded by PLIP

6 x ZMH: (6S,8R)-N-(3-bromo-4-fluorophenyl)-8-fluoro-10-methyl-11-oxo-1,3,4,7,8,9,10,11-octahydro-2H-pyrido[4',3':3,4]pyrazolo[1,5-a][1,4]diazepine-2-carboxamide(Non-covalent)

ZMH.3: 18 residues within 4Å: Chain A: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143 Chain C: S.124, V.127, W.128, T.131, A.135, P.137, P.141 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.28, A:Y.121, A:L.143, C:V.127 Hydrogen bonds: A:L.143, C:T.131 Halogen bonds: A:D.32 ZMH.6: 18 residues within 4Å: Chain A: S.124, V.127, W.128, T.131, A.135, P.137, P.141 Chain B: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.28, B:Y.121, B:L.143, A:V.127 Hydrogen bonds: B:L.143, A:T.131 Halogen bonds: B:D.32 ZMH.9: 18 residues within 4Å: Chain C: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143 Chain D: S.124, V.127, W.128, T.131, A.135, P.137, P.141 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.28, C:Y.121, C:L.143, D:V.127 Hydrogen bonds: C:L.143, D:T.131, D:T.131 Halogen bonds: C:D.32 ZMH.12: 17 residues within 4Å: Chain D: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, F.113, Y.121, I.142, L.143 Chain E: S.124, V.127, W.128, T.131, A.135 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:P.28, D:Y.121, D:L.143, E:V.127 Hydrogen bonds: D:L.143, E:T.131, E:T.131 Halogen bonds: D:D.32 ZMH.14: 18 residues within 4Å: Chain E: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, F.113, Y.121, I.142, L.143 Chain F: S.124, V.127, W.128, T.131, A.135, P.137 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:P.28, E:Y.121, E:L.143, F:V.127 Hydrogen bonds: E:L.143, F:T.131 Halogen bonds: E:D.32 ZMH.18: 19 residues within 4Å: Chain B: S.124, V.127, W.128, R.130, T.131, A.135, P.137, P.141 Chain F: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: B:V.127, F:P.28, F:Y.121 Hydrogen bonds: B:T.131, F:L.143 Halogen bonds: F:D.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuduk, S.D. et al., Diazepinone HBV capsid assembly modulators. Bioorg Med Chem Lett (2022)

Release Date

2023-04-12

Peptides

Capsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
D

D
E

E
B

F
C

Capsid protein

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