SMTL ID : 5t2p.1

Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-hexamer

Ligands

6 x K89: 4-fluoranyl-3-(4-oxidanylpiperidin-1-yl)sulfonyl-~{N}-[3,4,5-tris(fluoranyl)phenyl]benzamide(Non-covalent)

K89.1: 10 residues within 4Å: Chain A: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.25, A:F.110, A:L.140 Halogen bonds: A:W.102 K89.4: 17 residues within 4Å: Chain B: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain C: V.124, W.125, R.127, T.128, A.132, P.134 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:P.25, B:F.110, B:I.139, B:L.140, C:V.124, C:T.128 Hydrogen bonds: C:T.128, C:T.128 Water bridges: C:W.125 K89.8: 11 residues within 4Å: Chain C: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.25, C:F.110, C:L.140 Halogen bonds: C:D.29 K89.14: 17 residues within 4Å: Chain D: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140 Chain E: V.124, W.125, R.127, T.128, A.132, P.134 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:V.124, E:T.128, D:P.25, D:F.110, D:L.140, D:L.140 Hydrogen bonds: E:T.128, E:T.128 Water bridges: E:W.125 K89.20: 12 residues within 4Å: Chain E: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, I.139, L.140, S.141 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:P.25, E:F.110, E:L.140 K89.24: 15 residues within 4Å: Chain A: V.124, W.125, R.127, T.128, P.134 Chain F: P.25, D.29, L.30, T.33, W.102, I.105, S.106, F.110, Y.118, L.140 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:V.124, A:T.128, F:P.25, F:F.110, F:L.140 Hydrogen bonds: A:T.128, F:S.106 Water bridges: A:W.125 Halogen bonds: F:W.102

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

IPA.2: 8 residues within 4Å: Chain A: P.5, 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:P.5, A:F.97, B:L.60 Hydrogen bonds: A:K.96, B:D.64 IPA.3: 5 residues within 4Å: Chain A: S.17, L.19, S.21, L.95, Q.99 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.17 IPA.6: 6 residues within 4Å: Chain B: P.130, A.131, A.132, R.133, P.134, P.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.131 IPA.11: 4 residues within 4Å: Chain C: W.125, P.135, N.136, A.137 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.125, C:A.137 Hydrogen bonds: C:P.135, C:A.137 IPA.12: 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.13: 1 residues within 4Å: Chain C: D.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.29 IPA.17: 7 residues within 4Å: Chain C: K.96, F.97, L.100 Chain D: Q.57, L.60, C.61, D.64 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.97, C:L.100, D:L.60 Hydrogen bonds: C:K.96, C:K.96 IPA.22: 8 residues within 4Å: Chain E: Q.57, L.60, C.61, D.64 Chain F: P.5, K.96, F.97, L.100 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:P.5, F:F.97, E:L.60 Hydrogen bonds: F:K.96, E:D.64 IPA.23: 1 residues within 4Å: Chain E: D.29 No protein-ligand interaction detected (PLIP) IPA.26: 9 residues within 4Å: Chain A: P.130, A.131, A.132, R.133, P.134 Chain F: W.125, P.135, N.136, A.137 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:W.125, F:A.137 Hydrogen bonds: F:N.136, F:A.137

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

DMS.5: 4 residues within 4Å: Chain B: A.36, Y.38, R.39, D.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.40 Water bridges: B:A.41 Salt bridges: B:D.40 DMS.9: 9 residues within 4Å: Chain B: P.135, N.136, A.137 Chain C: P.130, A.131, A.132, R.133, P.134, P.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.137

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain B: R.28, D.29 Chain C: P.20, R.127 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.29 Water bridges: C:S.21, C:R.127 GOL.18: 3 residues within 4Å: Chain D: L.116, E.117, V.120 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.117 GOL.19: 3 residues within 4Å: Chain D: D.29 Chain E: P.20, R.127 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:R.127 Water bridges: D:D.29, D:D.29, D:D.29, D:D.32

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

CL.10: 2 residues within 4Å: Chain C: R.39, D.40 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: P.135, N.136, A.137 Chain E: R.133 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: R.39, D.40 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain E: R.39, D.40 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain F: L.37, D.40 Ligand excluded by PLIP

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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