SMTL ID : 4tqp.1

Human transthyretin (TTR) complexed with (R)-3-(9H-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide in a dual binding mode

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-tetramer

Ligands

4 x 48R: (2R)-3-[(9H-fluoren-9-ylideneamino)oxy]-2-methyl-N-(methylsulfonyl)propanamide(Non-covalent)

48R.1: 10 residues within 4Å: Chain A: K.15, L.17, P.24, S.52 Chain C: K.15, L.17, T.106, A.108, V.121 Ligands: 48R.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.15, A:L.17, C:T.106, C:A.108, C:V.121 Hydrogen bonds: A:K.15 Water bridges: A:K.15, A:S.52, C:R.104 48R.3: 19 residues within 4Å: Chain A: S.115 Chain B: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119, V.121 Chain D: K.15, L.17, A.108, L.110, S.117, T.119, V.121 Ligands: 48R.7 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:K.15, B:L.17, B:T.106, B:A.108, B:V.121, D:L.17, D:A.108, D:T.119, D:V.121 Hydrogen bonds: B:L.110, B:S.117, D:S.117 48R.5: 10 residues within 4Å: Chain A: K.15, L.17, T.106, A.108, V.121 Chain C: K.15, L.17, P.24, S.52 Ligands: 48R.1 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:K.15, C:L.17, A:T.106, A:A.108, A:V.121 Hydrogen bonds: C:K.15 Water bridges: C:K.15, C:S.52, A:R.104 48R.7: 19 residues within 4Å: Chain B: K.15, L.17, A.108, L.110, S.117, T.119, V.121 Chain C: S.115 Chain D: K.15, L.17, T.106, A.108, A.109, L.110, S.117, T.118, T.119, V.121 Ligands: 48R.3 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:L.17, B:A.108, B:T.119, B:V.121, D:K.15, D:L.17, D:T.106, D:A.108, D:V.121 Hydrogen bonds: B:S.117, D:L.110, D:S.117

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: L.110, L.111, S.112, S.115, Y.116, S.117 Chain B: S.117 Chain D: L.110, S.112, S.117 Ligands: GOL.6 8 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:S.117, B:S.117, A:S.112, A:S.117 Water bridges: C:S.117, C:S.117, A:S.117, A:S.117 GOL.4: 6 residues within 4Å: Chain A: S.85, P.86, Y.114 Chain B: T.96, N.98, Y.105 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.96, B:N.98, B:N.98, B:Y.105, A:S.85 Water bridges: A:Y.114 GOL.6: 11 residues within 4Å: Chain B: L.110, S.112, S.117 Chain C: L.110, L.111, S.112, S.115, Y.116, S.117 Chain D: S.117 Ligands: GOL.2 8 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:S.112, C:S.117, D:S.117, D:S.117 Water bridges: C:S.117, C:S.117, A:S.117, A:S.117 GOL.8: 6 residues within 4Å: Chain C: S.85, P.86, Y.114 Chain D: T.96, N.98, Y.105 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.85, D:T.96, D:N.98, D:N.98, D:Y.105 Water bridges: C:Y.114

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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