SMTL ID : 6ti9.1

Human transthyretin (TTR) complexed with (E)-3-(((3,5-dibromo-2-hydroxybenzylidene)amino)oxy)propanoic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x ND5: 3-[(~{E})-[3,5-bis(bromanyl)-2-oxidanyl-phenyl]methylideneamino]oxypropanoic acid(Non-covalent)

ND5.1: 19 residues within 4Å: Chain A: K.16, L.18, A.109, A.110, L.111, S.118, T.119, T.120 Chain C: K.16, L.18, T.107, A.109, A.110, L.111, S.118, T.119, T.120, V.122 Ligands: ND5.6 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:A.109, C:L.111, C:V.122, A:L.18 Halogen bonds: C:A.109, C:S.118 Water bridges: A:K.16 Salt bridges: A:K.16 ND5.3: 19 residues within 4Å: Chain B: K.16, L.18, A.109, A.110, L.111, S.118, T.119, T.120 Chain D: K.16, L.18, T.107, A.109, A.110, L.111, S.118, T.119, T.120, V.122 Ligands: ND5.8 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.111, B:L.18 Halogen bonds: D:S.118, B:S.118 Salt bridges: B:K.16 ND5.6: 19 residues within 4Å: Chain A: K.16, L.18, T.107, A.109, A.110, L.111, S.118, T.119, T.120, V.122 Chain C: K.16, L.18, A.109, A.110, L.111, S.118, T.119, T.120 Ligands: ND5.1 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.18, A:A.109, A:L.111, A:V.122 Water bridges: C:K.16 Salt bridges: C:K.16 Halogen bonds: A:A.109, A:S.118 ND5.8: 19 residues within 4Å: Chain B: K.16, L.18, T.107, A.109, A.110, L.111, S.118, T.119, T.120, V.122 Chain D: K.16, L.18, A.109, A.110, L.111, S.118, T.119, T.120 Ligands: ND5.3 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.18, B:L.111 Salt bridges: D:K.16 Halogen bonds: D:S.118, B:S.118

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: P.87, F.88, Y.115 Chain B: F.96, T.97, A.98, N.99, Y.106, V.123 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.97, B:T.97, B:Y.106, A:Y.115 Water bridges: B:T.97, B:N.99, B:Y.106, A:E.90, A:Y.115 GOL.7: 9 residues within 4Å: Chain C: P.87, F.88, Y.115 Chain D: F.96, T.97, A.98, N.99, Y.106, V.123 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:Y.115, D:T.97, D:T.97, D:Y.106 Water bridges: C:E.90, C:Y.115, D:T.97, D:N.99, D:Y.106

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 6 residues within 4Å: Chain B: R.22, I.27, N.28, Y.79, A.82, L.83 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.28, B:Y.79 Hydrogen bonds: B:R.22, B:Y.79 Water bridges: B:I.27 PGO.5: 10 residues within 4Å: Chain B: P.12, F.65, V.66, E.67, A.98, N.99, D.100, P.103, R.104, Y.106 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.65, B:Y.106 Hydrogen bonds: B:V.66, B:N.99, B:R.104, B:R.104, B:Y.106, B:Y.106 Water bridges: B:G.102 PGO.9: 6 residues within 4Å: Chain D: R.22, I.27, N.28, Y.79, A.82, L.83 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.28, D:Y.79 Hydrogen bonds: D:R.22, D:Y.79 Water bridges: D:I.27 PGO.10: 10 residues within 4Å: Chain D: P.12, F.65, V.66, E.67, A.98, N.99, D.100, P.103, R.104, Y.106 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.65, D:Y.106 Hydrogen bonds: D:V.66, D:N.99, D:R.104, D:R.104, D:Y.106, D:Y.106 Water bridges: D:G.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciccone, L. et al., Monoaryl derivatives as transthyretin fibril formation inhibitors: Design, synthesis, biological evaluation and structural analysis. Bioorg.Med.Chem. (2020)

Release Date

2020-10-21

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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