SMTL ID : 6uox.1

Structure of itraconazole-bound NPC1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.02 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.476, N.478, Q.489, T.536 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 8 residues within 4Å: Chain A: K.417, D.428, V.429, P.430, D.551, N.554, N.556, N.557 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.428

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.452 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.459 NAG.5: 1 residues within 4Å: Chain A: N.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.524 NAG.6: 2 residues within 4Å: Chain A: Q.438, N.598 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.438 Hydrogen bonds: A:Q.438 NAG.7: 2 residues within 4Å: Chain A: N.916, D.917 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.917 NAG.8: 1 residues within 4Å: Chain A: N.931 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.552 NAG.9: 2 residues within 4Å: Chain A: N.961, A.975 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.975 Hydrogen bonds: A:N.961 NAG.10: 4 residues within 4Å: Chain A: Y.475, N.968, N.1006, N.1008 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.475 Hydrogen bonds: A:N.968, A:N.1006

1 x QDG: 4-(3-bromo-4-{4-[4-({(2R,4S)-2-(2,4-dichlorophenyl)-2-[(1H-1,2,4-triazol-1-yl)methyl]-1,3-dioxolan-4-yl}methoxy)phenyl]piperazin-1-yl}phenyl)-2-[(2S)-butan-2-yl]-2,4-dihydro-3H-1,2,4-triazol-3-one(Non-covalent)

QDG.11: 20 residues within 4Å: Chain A: V.378, W.381, L.613, S.617, D.620, V.621, V.624, Y.628, L.684, I.685, I.687, E.688, Q.862, S.865, F.1087, Y.1088, V.1152, I.1220, F.1221, Y.1225 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.378, A:W.381, A:W.381, A:V.624, A:Y.1088, A:I.1220 Hydrogen bonds: A:Y.1088 pi-Stacking: A:Y.1225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, T. et al., Structural basis for itraconazole-mediated NPC1 inhibition. Nat Commun (2020)

Release Date

2020-01-15

Peptides

NPC intracellular cholesterol transporter 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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NPC intracellular cholesterol transporter 1