SMTL ID : 5wre.1

Hepatitis B virus core protein Y132A mutant in complex with heteroaryldihydropyrimidine (HAP_R01)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

6 x 7TL: (2S)-1-[[(4R)-4-(2-chloranyl-4-fluoranyl-phenyl)-5-methoxycarbonyl-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-4,4-bis(fluoranyl)pyrrolidine-2-carboxylic acid(Non-covalent)

7TL.1: 15 residues within 4Å: Chain A: 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.25, A:L.30, A:T.33, A:L.140 Hydrogen bonds: A:Y.118, A:L.140, A:S.141 pi-Stacking: A:F.23 7TL.5: 22 residues within 4Å: Chain B: 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 Chain C: V.124, W.125, R.127, T.128, A.132, R.133, P.134 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:P.25, B:L.30, B:T.33, B:L.140, C:V.124, C:R.127, C:P.134 Hydrogen bonds: B:L.140, B:S.141, C:T.128 pi-Stacking: B:F.23 7TL.10: 14 residues within 4Å: Chain C: F.23, P.25, D.29, L.30, T.33, L.37, W.102, I.105, S.106, F.110, Y.118, I.139, L.140, S.141 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.25, C:L.30, C:T.33, C:L.140 Hydrogen bonds: C:L.140, C:S.141 7TL.13: 22 residues within 4Å: Chain D: 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 Chain E: V.124, W.125, R.127, T.128, A.132, R.133, P.134 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:P.25, D:L.30, D:T.33, D:L.140, E:V.124, E:P.134 Hydrogen bonds: D:Y.118, D:L.140, D:S.141 7TL.16: 15 residues within 4Å: Chain E: 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 E Hydrophobic interactions: E:P.25, E:L.30, E:T.33, E:L.140 Hydrogen bonds: E:L.140, E:S.141 pi-Stacking: E:F.23 7TL.20: 22 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, I.105, S.106, T.109, F.110, Y.118, I.139, L.140, S.141 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:P.25, F:L.30, F:T.33, F:L.140, A:V.124, A:P.134 Hydrogen bonds: F:Y.118, F:L.140, F:S.141 Water bridges: F:Y.118, F:S.141, F:S.141

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

IPA.2: 9 residues within 4Å: Chain A: A.58, C.61, K.96, F.97, L.100 Chain B: Q.57, L.60, C.61, D.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.64, A:K.96 IPA.3: 7 residues within 4Å: Chain A: Q.57, L.60, C.61, D.64 Chain B: K.96, F.97, L.100 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.60, B:F.97, B:L.100 Hydrogen bonds: B:K.96, B:K.96 IPA.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:A.131, F:A.137 Hydrophobic interactions: F:W.125 IPA.11: 8 residues within 4Å: Chain C: Q.57, L.60, C.61, D.64 Chain D: C.61, K.96, F.97, L.100 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:D.64, D:K.96 Hydrophobic interactions: D:F.97, D:L.100 IPA.14: 8 residues within 4Å: Chain C: C.61, 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:F.97, C:L.100 Hydrogen bonds: C:K.96, C:K.96 IPA.17: 6 residues within 4Å: Chain E: A.36, L.37, Y.38, R.39, D.40, A.41 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:R.39, E:D.40 Hydrogen bonds: E:D.40, E:D.40, E:D.40, E:A.41 IPA.18: 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

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.2 Chain B: R.39, E.43 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain B: W.125, P.135, N.136, A.137 Chain C: P.130, A.131, A.132, R.133, P.135 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:R.133, C:R.133, B:P.138 Hydrogen bonds: B:A.137 GOL.9: 5 residues within 4Å: Chain B: A.35, A.36, L.37, R.39, D.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.39, B:D.40 Water bridges: B:A.35, B:R.39 GOL.12: 4 residues within 4Å: Chain C: D.2, D.4, K.7 Chain D: E.43 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.2, C:D.4, C:D.4, C:K.7 Water bridges: C:D.4 GOL.19: 7 residues within 4Å: Chain D: W.125, P.135, N.136, A.137 Chain E: P.130, A.131, R.133 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.137 Water bridges: D:A.137, D:P.138 GOL.21: 3 residues within 4Å: Chain F: A.131, A.132, R.133 No protein-ligand interaction detected (PLIP) GOL.22: 4 residues within 4Å: Chain A: T.12 Chain F: A.35, A.36, R.39 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Z. et al., Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms. Sci Rep (2017)

Release Date

2017-02-22

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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