SMTL ID : 8gbu.1 (2 other biounits)

Hepatitis B capsid Y132A mutant with compound AB-506

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

3 x YWE: (1-methyl-1H-1,2,4-triazol-3-yl)methyl {(1S)-4-[(3-chloro-4-fluorophenyl)carbamoyl]-7-fluoro-2,3-dihydro-1H-inden-1-yl}carbamate(Non-covalent)

YWE.1: 10 residues within 4Å: Chain A: P.28, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143, S.144 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.28, A:L.143 Hydrogen bonds: A:L.143, A:L.143 Halogen bonds: A:W.105 YWE.2: 6 residues within 4Å: Chain A: V.127, W.128, R.130, T.131, A.135, P.137 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.127, A:R.130, A:T.131 Hydrogen bonds: A:T.131 YWE.4: 12 residues within 4Å: Chain B: F.26, P.28, D.32, L.33, T.36, W.105, I.108, S.109, Y.121, I.142, L.143, S.144 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.28, B:I.108, B:Y.121, B:L.143, B:L.143 Hydrogen bonds: B:L.143, B:S.144 Halogen bonds: B:D.32

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: H.50 Chain B: P.53, R.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.115, B:R.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cole, A.G. et al., 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. (2023)

Release Date

2023-09-06

Peptides

Capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Capsid protein

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