SMTL ID : 8i71.1

Hepatitis B virus core protein Y132A mutant in complex with Linvencorvir (RG7907), a Hepatitis B Virus (HBV) Core Protein Allosteric Modulator (CpAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: L.37, R.39, D.40 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain D: N.136, A.137 Chain E: A.131, R.133 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: L.37, R.39, D.40 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain E: L.37, R.39, D.40 Ligand excluded by PLIP

9 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 8 residues within 4Å: Chain A: C.61, K.96, F.97, L.100 Chain B: Q.57, L.60, C.61, D.64 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.97, A:L.100, B:L.60 Hydrogen bonds: A:K.96, B:L.60 IPA.3: 7 residues within 4Å: Chain A: Q.57, L.60, C.61, D.64 Chain B: P.5, C.61, L.100 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.60, B:P.5, B:L.100 Water bridges: A:D.64, A:D.64 IPA.8: 6 residues within 4Å: Chain B: A.35, A.36, L.37, Y.38, R.39, D.40 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.39 Hydrogen bonds: B:D.40 Water bridges: B:A.41 IPA.13: 8 residues within 4Å: Chain C: P.5, K.96, F.97, L.100 Chain D: Q.57, L.60, C.61, D.64 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.5, C:F.97, C:L.100, D:L.60 Hydrogen bonds: C:K.96, C:K.96 IPA.14: 8 residues within 4Å: Chain C: Q.57, L.60, C.61, D.64 Chain D: P.5, K.96, F.97, L.100 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.5, D:F.97, C:L.60 Hydrogen bonds: D:K.96, C:D.64 IPA.15: 1 residues within 4Å: Chain C: D.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.29 IPA.19: 3 residues within 4Å: Chain C: P.50, H.51 Chain D: H.47 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.50 IPA.23: 8 residues within 4Å: Chain E: Q.57, L.60, C.61, D.64 Chain F: P.5, K.96, F.97, L.100 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.60, F:P.5, F:F.97, F:L.100 Hydrogen bonds: E:D.64, F:K.96 IPA.24: 5 residues within 4Å: Chain F: A.36, L.37, Y.38, R.39, D.40 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.39, F:D.40, F:D.40 Water bridges: F:A.41

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: P.130, A.131, R.133 Chain F: W.125, P.135, N.136, A.137 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:R.133, F:N.136, F:A.137 GOL.5: 3 residues within 4Å: Chain A: P.135, N.136, A.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.137 Water bridges: A:N.136, A:N.136 GOL.9: 5 residues within 4Å: Chain B: R.28, D.29 Chain C: P.20, I.126, R.127 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:R.127 Hydrogen bonds: B:D.29 GOL.10: 7 residues within 4Å: Chain B: W.125, P.135, N.136, A.137 Chain C: P.130, A.131, R.133 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.137 Water bridges: B:P.135, B:A.137, C:R.133

6 x OTI: 3-[(8~{a}~{S})-7-[[5-ethoxycarbonyl-4-(3-fluoranyl-2-methyl-phenyl)-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-3-oxidanylidene-5,6,8,8~{a}-tetrahydro-1~{H}-imidazo[1,5-a]pyrazin-2-yl]-2,2-dimethyl-propanoic acid(Non-covalent)

OTI.6: 13 residues within 4Å: Chain A: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.25, A:T.33, A:L.37, A:L.140 Hydrogen bonds: A:Y.118 Water bridges: A:L.140 OTI.11: 19 residues within 4Å: Chain B: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 Chain C: V.124, W.125, R.127, T.128, A.132, P.134 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:V.124, C:R.127, B:P.25, B:T.33, B:L.37, B:I.105, B:L.140 Hydrogen bonds: C:T.128 Water bridges: C:W.125, B:L.140 OTI.16: 13 residues within 4Å: Chain C: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.25, C:T.33, C:L.37, C:L.140 Hydrogen bonds: C:Y.118 Water bridges: C:L.140, C:L.140 OTI.20: 19 residues within 4Å: Chain D: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 Chain E: V.124, W.125, T.128, A.132, P.134, P.138 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:V.124, D:P.25, D:T.33, D:L.37, D:L.140 Hydrogen bonds: E:T.128 Water bridges: E:W.125, D:L.140, D:L.140 OTI.22: 13 residues within 4Å: Chain E: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.25, E:T.33, E:L.37, E:L.140 Water bridges: E:L.140, E:L.140 OTI.25: 19 residues within 4Å: Chain A: V.124, W.125, R.127, T.128, A.132, P.134 Chain F: F.23, P.25, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:P.25, F:T.33, F:L.37, F:L.140, A:V.124, A:R.127 Hydrogen bonds: F:Y.118 Water bridges: F:L.140, F:L.140, A:W.125

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 6 residues within 4Å: Chain A: A.35, A.36, L.37, Y.38, R.39, D.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.39, A:D.40 Salt bridges: A:D.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Discovery of Linvencorvir (RG7907), a Hepatitis B Virus Core Protein Allosteric Modulator, for the Treatment of Chronic HBV Infection. J.Med.Chem. (2023)

Release Date

2023-03-22

Peptides

Capsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Capsid protein

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