SMTL ID : 9vsr.1

The DCY1040 and TUG-891-bound structure of TMEM175

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x YN9: 3-{4-[(4-fluoro-4'-methyl[1,1'-biphenyl]-2-yl)methoxy]phenyl}propanoic acid(Non-covalent)

YN9.1: 7 residues within 4Å: Chain A: V.152, A.155, L.156, R.182, L.186, L.190 Ligands: CLR.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.152, A:L.190 Salt bridges: A:R.182 YN9.7: 7 residues within 4Å: Chain B: V.152, A.155, L.156, R.182, L.186, L.190 Ligands: CLR.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.152, B:A.155, B:L.156, B:L.186, B:L.190 Salt bridges: B:R.182

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 6 residues within 4Å: Chain A: I.148, L.190, P.193, A.194, F.197 Ligands: YN9.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.190, A:P.193, A:F.197 CLR.8: 6 residues within 4Å: Chain B: I.148, L.190, P.193, A.194, F.197 Ligands: YN9.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.148, B:L.190, B:P.193, B:F.197

2 x 01: (2S)-2-butyl-2-cyclohexyl-6,7-bis(fluoranyl)-5-[3-(1H-1,2,3,4-tetrazol-5-yl)propoxy]-3H-inden-1-one

01.3: 9 residues within 4Å: Chain A: L.111, L.114, M.118 Chain B: A.318, L.322, H.449, Q.452, P.456, C.457 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.318, B:L.322, A:L.111, A:L.114, A:L.114 01.4: 6 residues within 4Å: Chain A: A.318, H.449, Q.452, P.456 Chain B: L.111, M.118 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.318, A:P.456 Hydrogen bonds: A:H.449

3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.5: 1 residues within 4Å: Chain A: I.271 No protein-ligand interaction detected (PLIP) K.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.9: 2 residues within 4Å: Chain A: H.57 Chain B: E.282 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Structural insights into the activation of TMEM175 by small molecule. Neuron (2025)

Release Date

2025-09-17

Peptides

Endosomal/lysosomal proton channel TMEM175: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Endosomal/lysosomal proton channel TMEM175

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