SMTL ID : 7l0e.1

Crystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.2 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.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.180, B:H.241, B:H.313, B:H.527

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 21 residues within 4Å: Chain A: L.60, F.61, V.134, H.180, H.241, F.312, H.313, W.331, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, T.525, H.527 Ligands: FE2.1, XQ7.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.60, A:F.312, A:Y.338, A:L.341, A:F.418, A:F.418, A:L.437, A:L.439, A:P.444, A:V.524 Salt bridges: A:H.241, A:H.527 PLM.6: 21 residues within 4Å: Chain B: L.60, F.61, V.134, H.180, H.241, F.312, H.313, W.331, Y.338, L.341, E.417, F.418, L.437, L.439, F.442, P.444, V.524, T.525, H.527 Ligands: FE2.5, XQ7.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.60, B:F.61, B:F.312, B:Y.338, B:L.341, B:F.418, B:F.418, B:F.418, B:L.437, B:L.439, B:P.444, B:V.524 Salt bridges: B:H.241, B:H.527

2 x XQ7: (1R)-3-amino-1-{3-[(4,4-difluorocyclohexyl)methoxy]phenyl}propan-1-ol(Non-covalent)

XQ7.3: 13 residues within 4Å: Chain A: F.61, F.103, T.129, V.134, T.147, E.148, N.175, N.194, Y.239, I.259, Y.275, Y.338 Ligands: PLM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.61, A:F.103, A:F.103, A:T.129, A:E.148, A:I.259, A:Y.275 Hydrogen bonds: A:T.147, A:T.147 XQ7.7: 14 residues within 4Å: Chain B: F.61, F.103, T.129, V.134, T.147, E.148, T.149, N.194, Y.239, H.241, I.259, Y.275, Y.338 Ligands: PLM.6 12 PLIP interactions: 12 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, B:E.148, B:Y.239, B:Y.338

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: R.33, P.35, L.36, W.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.36, A:W.37 Salt bridges: A:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blum, E. et al., Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy. J.Med.Chem. (2021)

Release Date

2021-06-02

Peptides

Retinoid isomerohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retinoid isomerohydrolase

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