SMTL ID : 4tq8.1

Dual binding mode for 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid binding to Human transthyretin (TTR)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

4 x 7BD: 3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid(Non-covalent)

7BD.1: 15 residues within 4Å: Chain A: K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Chain C: K.15, L.17, A.108, L.110, V.121 Ligands: 7BD.5 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:L.17, C:A.108, C:V.121, A:L.17, A:T.106, A:A.108, A:V.121 Hydrogen bonds: A:S.117 Water bridges: A:L.110 7BD.2: 9 residues within 4Å: Chain B: K.15, L.17, T.106, A.108, V.121 Chain D: K.15, L.17, A.108 Ligands: 7BD.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.17, B:A.108, D:L.17, D:A.108 Water bridges: B:T.106 Salt bridges: D:K.15 7BD.5: 15 residues within 4Å: Chain A: K.15, L.17, A.108, L.110, V.121 Chain C: K.15, L.17, T.106, A.108, L.110, S.117, T.118, T.119, V.121 Ligands: 7BD.1 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.17, C:T.106, C:A.108, C:V.121, A:L.17, A:A.108, A:V.121 Hydrogen bonds: C:S.117 Water bridges: C:L.110 7BD.6: 9 residues within 4Å: Chain B: K.15, L.17, A.108 Chain D: K.15, L.17, T.106, A.108, V.121 Ligands: 7BD.2 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.17, B:A.108, D:L.17, D:A.108 Salt bridges: B:K.15 Water bridges: D:T.106

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain B: F.64, N.98, D.99, P.102, R.103, Y.105 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.98, B:N.98, B:R.103 EDO.4: 6 residues within 4Å: Chain A: P.86, F.87, Y.114 Chain B: T.96, N.98, Y.105 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.96, B:N.98, A:Y.114 EDO.7: 6 residues within 4Å: Chain D: F.64, N.98, D.99, P.102, R.103, Y.105 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.98, D:N.98, D:R.103 EDO.8: 6 residues within 4Å: Chain C: P.86, F.87, Y.114 Chain D: T.96, N.98, Y.105 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.114, D:T.96, D:N.98

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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