SMTL ID : 5yve.1

Crystal structure of human P2X3 receptor in complex with the AF-219 negative allosteric modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.108, E.110, E.155, D.157 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.110, A:E.110, A:D.157 MG.6: 4 residues within 4Å: Chain B: E.108, E.110, E.155, D.157 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.110, B:E.110, B:D.157 MG.11: 4 residues within 4Å: Chain C: E.108, E.110, E.155, D.157 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.110, C:E.110, C:D.157

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain C: I.322 Ligands: NA.7, NA.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.322 NA.7: 3 residues within 4Å: Chain A: I.322 Ligands: NA.2, NA.12 No protein-ligand interaction detected (PLIP) NA.12: 3 residues within 4Å: Chain B: I.322 Ligands: NA.2, NA.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322

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

NAG.3: 3 residues within 4Å: Chain A: E.168, N.169 Chain C: P.127 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.168 Hydrogen bonds: A:N.169 NAG.4: 3 residues within 4Å: Chain A: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:S.291, A:S.291 NAG.8: 3 residues within 4Å: Chain A: P.127 Chain B: E.168, N.169 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.168 Hydrogen bonds: B:N.169 NAG.9: 3 residues within 4Å: Chain B: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.289, B:S.291, B:S.291 NAG.13: 3 residues within 4Å: Chain B: P.127 Chain C: E.168, N.169 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.168 Hydrogen bonds: C:N.169 NAG.14: 3 residues within 4Å: Chain C: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.289, C:S.291, C:S.291

3 x AF9: 5-[2,4-bis(azanyl)pyrimidin-5-yl]oxy-2-methoxy-4-propan-2-yl-benzenesulfonamide(Non-covalent)

AF9.5: 15 residues within 4Å: Chain A: L.264, D.265, S.266, V.273, S.274, P.275, G.276 Chain B: S.58, V.60, K.175, N.176, S.177, G.188, N.189, L.190 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.60, B:K.175, B:L.190, A:L.264, A:D.265 Hydrogen bonds: B:N.176, B:N.189, B:N.189, B:L.190, A:S.266 AF9.10: 15 residues within 4Å: Chain B: L.264, D.265, S.266, V.273, S.274, P.275, G.276 Chain C: S.58, V.60, K.175, N.176, S.177, G.188, N.189, L.190 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.60, C:K.175, C:L.190, B:L.264, B:D.265 Hydrogen bonds: C:N.176, C:N.189, C:N.189, C:L.190, B:S.266 AF9.15: 15 residues within 4Å: Chain A: S.58, V.60, K.175, N.176, S.177, G.188, N.189, L.190 Chain C: L.264, D.265, S.266, V.273, S.274, P.275, G.276 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.60, A:K.175, A:L.190, C:L.264, C:D.265 Hydrogen bonds: A:N.176, A:N.189, A:N.189, A:L.190, C:S.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Druggable negative allosteric site of P2X3 receptors. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-04

Peptides

P2X purinoceptor 3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

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