SMTL ID : 5gmz.1

Hepatitis B virus core protein Y132A mutant in complex with 4-methyl heteroaryldihydropyrimidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

IPA.1: 9 residues within 4Å: Chain A: P.5, C.61, K.96, F.97, L.100 Chain B: Q.57, L.60, C.61, D.64 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.5, A:F.97, A:L.100, B:L.60 Hydrogen bonds: A:K.96, B:D.64 IPA.2: 8 residues within 4Å: Chain A: Q.57, L.60, C.61, D.64 Chain B: P.5, K.96, F.97, L.100 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.5, B:F.97, B:L.100, A:L.60 Hydrogen bonds: B:K.96, B:K.96 IPA.3: 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: 2 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:W.125 Hydrogen bonds: F:A.137, A:A.131 IPA.4: 4 residues within 4Å: Chain A: A.36, L.37, R.39, D.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.39, A:D.40, A:D.40 IPA.9: 8 residues within 4Å: Chain C: Q.57, L.60, C.61, D.64 Chain D: P.5, K.96, F.97, L.100 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.5, D:F.97, D:L.100, C:L.60 Hydrogen bonds: D:K.96, C:D.64 IPA.11: 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.12: 3 residues within 4Å: Chain D: D.29 Chain E: I.126, R.127 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.126 IPA.15: 6 residues within 4Å: Chain E: A.35, L.37, Y.38, R.39, D.40, A.41 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:R.39 Hydrogen bonds: E:Y.38, E:D.40, E:A.41 IPA.16: 8 residues within 4Å: Chain E: Q.57, L.60, C.61, D.64 Chain F: C.61, K.96, F.97, L.100 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.97, F:L.100, E:L.60 Hydrogen bonds: F:K.96, F:K.96 IPA.17: 7 residues within 4Å: Chain D: W.125, P.135, N.136, A.137 Chain E: P.130, A.131, R.133 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.136, D:A.137 IPA.18: 4 residues within 4Å: Chain E: W.125, P.135, N.136, A.137 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.125, E:A.137 Hydrogen bonds: E:P.135

7 x 6XU: (2S)-4,4-difluoro-1-[[(4S)-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1H-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid(Non-covalent)

6XU.5: 14 residues within 4Å: Chain A: F.23, P.25, D.29, L.30, T.33, L.37, W.102, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.25, A:L.30, A:T.33 Hydrogen bonds: A:Y.118, A:L.140, A:S.141 Water bridges: A:S.141 Halogen bonds: A:D.29 6XU.6: 10 residues within 4Å: Chain A: W.71, T.74, N.75, E.77 Chain B: L.76, D.78, A.80, S.81, L.84, V.85 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.71, A:N.75 6XU.8: 21 residues within 4Å: Chain B: F.23, P.25, D.29, L.30, T.33, L.37, W.102, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 Chain C: V.124, W.125, R.127, T.128, A.132, R.133, P.134 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.25, B:L.30, B:T.33 Hydrogen bonds: B:L.140, B:S.141 Halogen bonds: B:D.29 6XU.10: 15 residues within 4Å: Chain C: F.23, P.25, D.29, L.30, T.33, L.37, W.102, I.105, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.25, C:L.30, C:T.33, C:I.105 Hydrogen bonds: C:L.140, C:S.141 Halogen bonds: C:D.29 6XU.14: 21 residues within 4Å: Chain D: F.23, P.25, D.29, L.30, T.33, L.37, W.102, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 Chain E: V.124, W.125, R.127, T.128, A.132, R.133, P.134 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:P.25, D:L.30, D:T.33, D:F.110, E:P.134 Hydrogen bonds: D:Y.118, D:L.140, D:S.141 Halogen bonds: D:D.29 6XU.19: 14 residues within 4Å: Chain E: F.23, P.25, D.29, L.30, T.33, L.37, W.102, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:P.25, E:L.30, E:T.33 Hydrogen bonds: E:L.140, E:S.141 Water bridges: E:S.141 Halogen bonds: E:D.29 6XU.21: 21 residues within 4Å: Chain A: V.124, W.125, R.127, T.128, A.132, R.133, P.134 Chain F: F.23, P.25, D.29, L.30, T.33, L.37, W.102, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:P.25, F:L.30, F:T.33, A:P.134 Hydrogen bonds: F:Y.118, F:L.140, F:S.141 Halogen bonds: F:D.29

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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: 1 interactions with chain C, 3 interactions with chain B Water bridges: C:R.133, B:P.135, B:A.137 Hydrogen bonds: B:A.137 GOL.20: 4 residues within 4Å: Chain F: P.130, A.131, A.132, R.133 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.133

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

CL.13: 1 residues within 4Å: Chain D: D.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiu, Z. et al., Design and Synthesis of Orally Bioavailable 4-Methyl Heteroaryldihydropyrimidine Based Hepatitis B Virus (HBV) Capsid Inhibitors. J.Med.Chem. (2016)

Release Date

2016-08-10

Peptides

Core protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Core protein

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