SMTL ID : 8khu.1

Hepatitis B virus core protein Y132A mutant in complex with THPP derivatives 48

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-heptamer

Ligands

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

IPA.1: 6 residues within 4Å: Chain A: P.5, K.96, L.100 Chain B: Q.57, L.60, D.64 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.5, A:L.100, B:L.60 Hydrogen bonds: A:K.96, B:D.64 IPA.2: 7 residues within 4Å: Chain A: Q.57, L.60, C.61, D.64 Chain B: P.5, K.96, L.100 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.5, B:L.100, A:L.60 Hydrogen bonds: B:K.96, B:K.96 IPA.4: 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 Hydrogen bonds: B:D.40, B:D.40 Water bridges: B:A.41 IPA.6: 8 residues within 4Å: Chain C: Q.57, L.60, C.61, D.64 Chain D: P.5, K.96, F.97, L.100 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.60, D:P.5 Hydrogen bonds: C:D.64, D:K.96 IPA.8: 8 residues within 4Å: Chain C: P.5, K.96, F.97, L.100 Chain D: Q.57, L.60, C.61, D.64 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.60, C:P.5, C:L.100 Hydrogen bonds: C:K.96, C:K.96 IPA.10: 7 residues within 4Å: Chain E: Q.57, L.60, C.61, D.64 Chain F: P.5, K.96, L.100 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:P.5, F:L.100, E:L.60 Hydrogen bonds: F:K.96, F:K.96 IPA.11: 8 residues within 4Å: Chain E: P.5, K.96, F.97, L.100 Chain F: Q.57, L.60, C.61, D.64 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:P.5, E:L.100 Hydrogen bonds: E:K.96, F:D.64

6 x VX0: (6~{S},7~{R})-6,7-dimethyl-3-(2-oxidanylidenepyrrolidin-1-yl)-~{N}-[3,4,5-tris(fluoranyl)phenyl]-6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazine-5-carboxamide(Non-covalent)

VX0.3: 10 residues within 4Å: Chain A: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, Y.118, L.140 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.23, A:P.25, A:L.140 Hydrogen bonds: A:L.140 Halogen bonds: A:D.29, A:W.102 VX0.5: 18 residues within 4Å: Chain B: F.23, P.25, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain C: S.121, V.124, W.125, R.127, T.128, A.132, P.134 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.124, C:W.125, C:A.132, B:F.23, B:P.25 Hydrogen bonds: C:T.128, B:L.140 Halogen bonds: B:W.102 VX0.7: 11 residues within 4Å: Chain C: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, Y.118, I.139, L.140 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.23, C:P.25, C:Y.118, C:L.140 Hydrogen bonds: C:L.140 Halogen bonds: C:D.29 VX0.9: 18 residues within 4Å: Chain D: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, Y.118, I.139, L.140 Chain E: S.121, V.124, W.125, R.127, T.128, A.132, P.134 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:V.124, E:W.125, E:T.128, E:A.132, D:F.23, D:P.25, D:Y.118, D:L.140 Hydrogen bonds: E:T.128, D:L.140 VX0.12: 11 residues within 4Å: Chain E: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, Y.118, I.139, L.140 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.23, E:P.25, E:Y.118, E:L.140 Hydrogen bonds: E:L.140 Halogen bonds: E:D.29 VX0.13: 18 residues within 4Å: Chain A: S.121, V.124, W.125, R.127, T.128, A.132, P.134 Chain F: F.23, P.25, D.29, L.30, T.33, W.102, I.105, S.106, Y.118, I.139, L.140 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:F.23, F:P.25, F:Y.118, F:L.140, A:W.125, A:T.128, A:A.132 Hydrogen bonds: F:L.140, A:T.128 Halogen bonds: F:D.29

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain E: M.1 Chain F: R.28 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.28, F:R.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kou, B. et al., Discovery of 4,5,6,7-Tetrahydropyrazolo[1.5-a]pyrizine Derivatives as Core Protein Allosteric Modulators (CpAMs) for the Inhibition of Hepatitis B Virus. J.Med.Chem. (2023)

Release Date

2023-10-25

Peptides

Capsid protein: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Capsid protein

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