SMTL ID : 4tqi.1

Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid in a dual binding mode

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

4 x 6BD: (2S)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methylpropanoic acid(Non-covalent)

6BD.1: 11 residues within 4Å: Chain A: K.15, L.17, T.106, A.108, V.121 Chain C: K.15, L.17, T.106, A.108, V.121 Ligands: 6BD.5 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:L.17, C:T.106, C:A.108, C:V.121, A:K.15, A:L.17, A:T.106, A:A.108, A:V.121 Water bridges: C:T.106, A:K.15, A:K.15 Salt bridges: A:K.15 6BD.2: 10 residues within 4Å: Chain B: K.15, L.17, A.108 Chain D: M.13, K.15, L.17, T.106, A.108, V.121 Ligands: 6BD.6 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.17, D:T.106, D:A.108, B:K.15, B:L.17, B:A.108 Water bridges: D:T.106, B:K.15 Salt bridges: B:K.15 6BD.5: 11 residues within 4Å: Chain A: K.15, L.17, T.106, A.108, V.121 Chain C: K.15, L.17, T.106, A.108, V.121 Ligands: 6BD.1 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:K.15, C:L.17, C:T.106, C:A.108, C:V.121, A:L.17, A:T.106, A:A.108, A:V.121 Water bridges: C:K.15, C:K.15, A:T.106 Salt bridges: C:K.15 6BD.6: 10 residues within 4Å: Chain B: M.13, K.15, L.17, T.106, A.108, V.121 Chain D: K.15, L.17, A.108 Ligands: 6BD.2 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.17, B:T.106, B:A.108, D:K.15, D:L.17, D:A.108 Water bridges: B:T.106, D:K.15 Salt bridges: D:K.15

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: P.86, F.87, Y.114 Chain B: T.96, N.98, Y.105 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.96, B:N.98, B:Y.105, A:P.86 Water bridges: A:Y.114 GOL.4: 6 residues within 4Å: Chain A: W.41, K.70 Chain B: K.70, E.72, H.90, E.92 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.70, B:E.92, A:K.70 Water bridges: A:K.35 GOL.7: 6 residues within 4Å: Chain C: P.86, F.87, Y.114 Chain D: T.96, N.98, Y.105 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.96, D:N.98, D:Y.105, C:P.86 Water bridges: C:Y.114 GOL.8: 6 residues within 4Å: Chain C: W.41, K.70 Chain D: K.70, E.72, H.90, E.92 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.70, D:K.70, D:E.92 Water bridges: C:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciccone, L. et al., X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors. J Enzyme Inhib Med Chem (2015)

Release Date

2015-06-24

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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