SMTL ID : 8doc.1

Crystal structure of RPE65 in complex with compound 16e and palmitate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.180, H.241, H.313, H.527 Ligands: PLM.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.180, A:H.241, A:H.313, A:H.527 FE2.5: 5 residues within 4Å: Chain B: H.180, H.241, H.313, H.527 Ligands: PLM.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.180, B:H.241, B:H.313, B:H.527

2 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.2: 7 residues within 4Å: Chain A: Y.299, I.300, N.301, N.302, I.374, L.395, E.399 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.374, A:L.395, A:E.399 Hydrogen bonds: A:N.301, A:N.301 Water bridges: A:Y.299, A:N.301, A:N.301, A:E.399 CXS.6: 7 residues within 4Å: Chain B: Y.299, I.300, N.301, N.302, I.374, L.395, E.399 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.374, B:L.395, B:E.399 Hydrogen bonds: B:N.301, B:N.301 Water bridges: B:Y.299, B:N.301, B:N.301, B:E.399

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 21 residues within 4Å: Chain A: L.60, F.61, V.134, H.180, H.241, F.312, H.313, Y.338, E.417, F.418, L.437, L.439, F.442, P.444, P.467, V.524, T.525, F.526, H.527 Ligands: FE2.1, SYL.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.60, A:F.61, A:F.312, A:F.312, A:Y.338, A:F.418, A:F.418, A:F.418, A:L.437, A:L.439, A:V.524 Salt bridges: A:H.241, A:H.313, A:H.527 PLM.7: 21 residues within 4Å: Chain B: L.60, F.61, V.134, H.180, H.241, F.312, H.313, Y.338, E.417, F.418, L.437, L.439, F.442, P.444, P.467, V.524, T.525, F.526, H.527 Ligands: FE2.5, SYL.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.60, B:F.61, B:F.312, B:F.312, B:Y.338, B:F.418, B:F.418, B:F.418, B:L.437, B:L.439, B:V.524 Salt bridges: B:H.241, B:H.313, B:H.527

2 x SYL: (1R)-1-[3-(cyclohexylmethoxy)phenyl]-3-(methylamino)propan-1-ol(Non-covalent)

SYL.4: 15 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, Y.239, H.241, I.259, Y.275, Y.338 Ligands: PLM.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.61, A:F.103, A:F.103, A:T.129, A:E.148, A:T.149, A:I.259, A:Y.275 SYL.8: 15 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.175, N.194, Y.239, H.241, I.259, Y.275, Y.338 Ligands: PLM.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.61, B:F.103, B:F.103, B:T.129, B:E.148, B:T.149, B:I.259, B:Y.275 Hydrogen bonds: B:T.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bassetto, M. et al., Tuning the Metabolic Stability of Visual Cycle Modulators through Modification of an RPE65 Recognition Motif. J.Med.Chem. (2023)

Release Date

2023-05-24

Peptides

Retinoid isomerohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Retinoid isomerohydrolase

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