SMTL ID : 9m8p.1

GPR3 dimer with antagonist AF64394

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x 5YM: (Z)-N-(2-hydroxyethyl)octadec-9-enamide(Non-covalent)

5YM.1: 13 residues within 4Å: Chain A: L.171, L.217, H.220, V.237, L.240, F.244, T.245, I.248, L.322, F.326, W.384, T.388, L.407 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.244, A:I.248, A:L.322, A:W.384, A:W.384, A:T.388 Hydrogen bonds: A:H.220 5YM.9: 14 residues within 4Å: Chain B: L.171, L.217, H.220, V.237, L.240, F.244, T.245, I.248, L.322, F.326, V.329, W.384, F.387, L.407 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.244, B:I.248, B:I.248, B:L.322, B:V.329, B:W.384, B:F.387

4 x 1DO: 1-DODECANOL(Non-covalent)

1DO.2: 3 residues within 4Å: Chain A: V.389, Y.390, L.393 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.390, A:L.393 Hydrogen bonds: A:L.393 1DO.7: 4 residues within 4Å: Chain A: W.299, V.321, I.324 Chain B: L.393 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.299, A:V.321, A:I.324, B:L.393 1DO.10: 2 residues within 4Å: Chain B: W.299, I.324 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.299, B:I.324 1DO.11: 3 residues within 4Å: Chain B: V.389, Y.390, L.393 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.390

4 x 01: (4Z)-oct-4-en-1-ol(Non-functional Binders)

01.3: 3 residues within 4Å: Chain A: V.279 Ligands: 02.6, 01.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.279 01.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 01.8: 3 residues within 4Å: Chain B: A.338 Ligands: 01.3, 02.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.338 01.12: 1 residues within 4Å: Ligands: 02.4 No protein-ligand interaction detected (PLIP)

2 x 02: N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine

02.4: 11 residues within 4Å: Chain A: Q.335, A.338, Q.339, R.342 Chain B: L.252, V.256, Y.259, L.260, M.280, L.283 Ligands: 01.12 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.252, B:L.283, A:A.338 Hydrogen bonds: A:Q.335, A:Q.335, A:R.342, A:R.342 02.6: 10 residues within 4Å: Chain A: L.252, V.256, Y.259, L.260, M.280 Chain B: Q.335, Q.339, R.342 Ligands: 01.3, 01.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.335, B:R.342, B:R.342 Hydrophobic interactions: A:L.252, A:V.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, C. et al., GPR3 dimer with antagonist AF64394. To Be Published

Release Date

2025-09-24

Peptides

Soluble cytochrome b562,G-protein coupled receptor 3: 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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Soluble cytochrome b562,G-protein coupled receptor 3

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