SMTL ID : 9ik1.1

Cryo-EM structure of the human P2X3 receptor-compound 26a complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x 01: 4-[2-cyclopropyl-7-[[(1~{R})-1-naphthalen-2-ylethyl]amino]-[1,2,4]triazolo[1,5-a]pyrimidin-5-yl]piperazine-1-carboxamide

01.1: 8 residues within 4Å: Chain A: Y.32, F.33, T.325, S.326, V.329 Chain C: V.321 Ligands: 01.7, 01.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.33 01.7: 7 residues within 4Å: Chain A: T.325 Chain B: Y.32, F.33, S.326, V.329 Ligands: 01.1, 01.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.32, B:F.33 01.13: 5 residues within 4Å: Chain C: Y.32, F.33, S.326 Ligands: 01.1, 01.7 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.32, C:Y.32, C:F.33

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.2: 11 residues within 4Å: Chain A: K.58, K.60, T.167, F.169, M.195 Chain B: D.153, V.269, S.270, R.276, K.294 Ligands: MG.12 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:N.274, A:T.167, A:T.167 Salt bridges: B:R.276, B:K.294, B:K.294, A:K.58, A:K.58, A:K.58, A:K.60 pi-Cation interactions: A:K.60 ATP.8: 12 residues within 4Å: Chain B: K.58, V.59, K.60, T.167, F.169, M.195 Chain C: D.153, V.269, N.274, R.276, K.294 Ligands: MG.18 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:N.274, B:T.167, B:T.167 Salt bridges: C:R.276, C:K.294, C:K.294, B:K.58, B:K.58, B:K.58, B:K.60 pi-Cation interactions: B:K.60 ATP.14: 12 residues within 4Å: Chain A: D.153, V.269, S.270, N.274, R.276, K.294 Chain C: K.58, K.60, T.167, F.169, M.195 Ligands: MG.6 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:N.274, C:T.167, C:T.167 Salt bridges: A:R.276, A:K.294, A:K.294, C:K.58, C:K.58, C:K.58, C:K.60 pi-Cation interactions: C:K.60

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.3: 3 residues within 4Å: Chain A: M.161, E.164, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165 NAG.4: 3 residues within 4Å: Chain A: L.187, N.189, F.207 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: M.283, N.285, S.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.287, A:S.287 NAG.9: 3 residues within 4Å: Chain B: M.161, N.165 Chain C: L.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.165 NAG.10: 5 residues within 4Å: Chain B: L.187, N.189, F.207, D.249, I.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.249 NAG.11: 2 residues within 4Å: Chain B: N.285, S.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.287 NAG.15: 3 residues within 4Å: Chain C: M.161, E.162, N.165 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:M.161 NAG.16: 3 residues within 4Å: Chain C: L.187, N.189, F.207 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain C: N.285, S.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.285, C:S.287

3 x MG: MAGNESIUM ION

MG.6: 2 residues within 4Å: Chain A: D.153 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.153 MG.12: 2 residues within 4Å: Chain B: D.153 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.153 MG.18: 2 residues within 4Å: Chain C: D.153 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, G.R. et al., Discovery of Triazolopyrimidine Derivatives as Selective P2X3 Receptor Antagonists Binding to an Unprecedented Allosteric Site as Evidenced by Cryo-Electron Microscopy. J.Med.Chem. (2024)

Release Date

2024-09-04

Peptides

P2X purinoceptor 3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor 3