SMTL ID : 7w9q.1

Crystal structure of V30M-TTR in complex with naringenin derivative-14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x 90Q: (2~{R})-2-(3-chloranyl-4-oxidanyl-phenyl)-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one(Non-covalent)

90Q.1: 14 residues within 4Å: Chain A: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Chain C: K.47, L.49, L.142, S.149 Ligands: 90Q.5 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.49, C:L.49, C:L.142 Hydrogen bonds: A:K.47, A:S.149, C:K.47 Water bridges: C:S.149, C:S.149 90Q.3: 13 residues within 4Å: Chain B: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Chain D: K.47, A.140, L.142, S.149, T.151 Ligands: 90Q.7 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:A.140, D:L.142, D:T.151, B:L.49 Hydrogen bonds: D:K.47, B:K.47, B:S.149 Water bridges: D:S.149, D:S.149 90Q.5: 14 residues within 4Å: Chain A: K.47, L.49, L.142, S.149 Chain C: K.47, L.49, T.138, A.140, L.142, S.149, T.150, T.151, V.153 Ligands: 90Q.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.49, A:L.142, C:L.49 Hydrogen bonds: A:K.47, C:K.47, C:S.149 Water bridges: A:S.149, A:S.149 90Q.7: 13 residues within 4Å: Chain B: K.47, A.140, L.142, S.149, T.151 Chain D: K.47, L.49, A.140, L.142, S.149, T.150, T.151 Ligands: 90Q.3 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.49, B:A.140, B:L.142, B:T.151 Hydrogen bonds: D:K.47, D:S.149, B:K.47 Water bridges: B:S.149, B:S.149

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: E.98, D.131 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.98, A:D.131, A:D.131 CA.4: 3 residues within 4Å: Chain B: E.98, N.130, D.131 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.98 CA.6: 2 residues within 4Å: Chain C: E.98, D.131 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.98, C:D.131, C:D.131 CA.8: 3 residues within 4Å: Chain D: E.98, N.130, D.131 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizuguchi, M. et al., Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis. J.Med.Chem. (2022)

Release Date

2022-12-14

Peptides

Transthyretin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Transthyretin

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