SMTL ID : 5wiu.1

Structure of the human D4 Dopamine receptor in complex with Nemonapride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x AQD: Nemonapride(Non-covalent)

AQD.1: 20 residues within 4Å: Chain A: V.91, L.94, F.95, L.115, M.116, D.119, V.120, C.123, T.124, C.189, L.191, V.197, S.200, S.201, S.204, F.365, F.366, H.369, T.389, Y.393 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.91, A:F.95, A:F.95, A:L.115, A:V.120, A:L.191, A:F.365, A:F.365, A:T.389 Hydrogen bonds: A:D.119, A:D.119, A:S.200, A:S.200, A:Y.393 Salt bridges: A:D.119 Halogen bonds: A:V.197

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: Y.147, G.152, S.153, R.155, Q.156 Ligands: GOL.23 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.147, A:S.153, A:Q.156 Water bridges: A:R.154 Salt bridges: A:R.155 PO4.3: 2 residues within 4Å: Chain A: Q.224, R.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.224 Salt bridges: A:R.345 PO4.4: 1 residues within 4Å: Chain A: L.89 No protein-ligand interaction detected (PLIP)

9 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 10 residues within 4Å: Chain A: V.63, T.71, N.74, S.75, V.78, S.79, A.82, L.157, W.164 Ligands: PEG.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.63, A:V.78, A:A.82, A:L.157, A:W.164 Hydrogen bonds: A:T.71 OLA.6: 11 residues within 4Å: Chain A: A.40, A.41, G.44, L.47, L.48, A.51, E.99, S.386, W.390, V.394 Ligands: OLA.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.47, A:L.48, A:A.51, A:W.390, A:W.390, A:W.390, A:V.394 Hydrogen bonds: A:E.99 OLA.7: 4 residues within 4Å: Chain A: R.383, S.386, A.387 Ligands: OLA.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.383, A:A.387 Hydrogen bonds: A:S.386, A:S.386 OLA.8: 5 residues within 4Å: Chain A: F.128, C.131, L.166, Y.199, C.203 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.128, A:L.166 OLA.9: 10 residues within 4Å: Chain A: G.55, L.58, V.59, S.62, P.400, T.404, V.405, F.410, V.413, F.414 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.58, A:V.59, A:P.400, A:T.404, A:V.405, A:V.413, A:F.414, A:F.414 OLA.10: 10 residues within 4Å: Chain A: L.213, Y.216, W.217, F.220, Q.224, R.345, P.352, V.355, G.356, L.359 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.216, A:F.220, A:F.220, A:P.352, A:P.352, A:V.355, A:L.359 Hydrogen bonds: A:Q.224 Salt bridges: A:R.345 OLA.11: 3 residues within 4Å: Chain A: F.138, A.142, V.143 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.143 OLA.12: 5 residues within 4Å: Chain A: G.356, A.357, L.360, V.405, F.406 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.357, A:L.360, A:V.405, A:F.406, A:F.406 OLA.13: 5 residues within 4Å: Chain A: F.206, C.209, I.370, T.371, L.374 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.370, A:L.374

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 2 residues within 4Å: Chain A: P.364, L.384 No protein-ligand interaction detected (PLIP) PEG.15: 2 residues within 4Å: Chain A: V.198, L.374 No protein-ligand interaction detected (PLIP) PEG.16: 4 residues within 4Å: Chain A: M.118, M.121, A.168, L.175 No protein-ligand interaction detected (PLIP) PEG.17: 2 residues within 4Å: Chain A: V.46, I.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.93 PEG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.19: 3 residues within 4Å: Chain A: L.107, S.108 Ligands: PEG.20 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain A: S.108, R.110, L.111 Ligands: PEG.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.108 Water bridges: A:S.108, A:R.110 PEG.21: 4 residues within 4Å: Chain A: W.164, L.165, A.168 Ligands: OLA.5 No protein-ligand interaction detected (PLIP) PEG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 6 residues within 4Å: Chain A: P.72, R.137, A.140, R.155, Q.156 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.137, A:R.137, A:R.155, A:Q.156 Water bridges: A:R.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science (2017)

Release Date

2017-10-18

Peptides

D(4) dopamine receptor, soluble cytochrome b562 chimera: 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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D(4) dopamine receptor, soluble cytochrome b562 chimera

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