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Science 330 (6007): 1091-1095

Copyright © 2010 by the American Association for the Advancement of Science

Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist

Ellen Y. T. Chien1, Wei Liu1, Qiang Zhao1, Vsevolod Katritch2, Gye Won Han1, Michael A. Hanson3, Lei Shi4, Amy Hauck Newman5, Jonathan A. Javitch6, Vadim Cherezov1, and Raymond C. Stevens1,*

1 Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
2 Skaggs School of Pharmacy and Pharmaceutical Sciences, and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
3 Receptos, 10835 Road to the Cure, Suite 205, San Diego, CA 92121, USA.
4 Department of Physiology and Biophysics and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY 10021, USA.
5 Medicinal Chemistry Section, National Institute on Drug Abuse–Intramural Research Program, Baltimore, MD 21224, USA.
6 Center for Molecular Recognition and Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, 630 West 168th, New York, NY 10032, USA.


Figure 1
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Fig. 1. Overall D3R structure with eticlopride and comparison with β2AR structure. (A) A model of the D3R with the bound ligand eticlopride in space-filling representation; ECL2 is shown in green, ICL2 in purple, and disulfide bonds in brown (conformation of chain A shown). (B) Comparison of the TM domains of D3R (brown) and β2AR (blue; PDB ID: 2RH1).

 

Figure 2
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Fig. 2. Conformation of ICL2 and ionic lock motif in D3R and other GPCR structures. As also seen in (A) the inactive Rhodopsin structure (PDB ID: 1U19), the conserved ionic lock motif D[E]RY is in a "locked" conformation in (B) the D3R structure, i.e., with a salt bridge formed between Arg1283.50 and Glu3246.30. In addition, the side chain of Tyr138 in the ICL2 {alpha} helix of the D3R is inserted into the seven-TM bundle forming hydrogen bonds with Thr642.39, Arg1283.50, and Asp1273.49 (distances of 3.0, 3.2, and 3.2 Å, respectively), potentially stabilizing the ionic lock. There is no salt bridge between Arg3.50 and Glu6.30 (and hence the "ionic lock" is "broken") in other crystal structures of GPCR shown in (C) β1AR (PDB ID: 2VT4), (D) β2AR (PDB ID: 2RH1), and (E) A2AAR (PDB ID: 3EML). In both the β1AR and A2AAR structures, however, the corresponding Tyr residue in ICL2 that aligns to Tyr138 in D3R forms two hydrogen bonds with the Asp3.49 and Arg3.50 side chains even in the absence of the closed ionic lock conformation. Salt bridges and hydrogen bond interactions are shown as dashed lines.

 

Figure 3
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Fig. 3. Structural diversity of ligand binding sites in GPCR structures. (A) Close-up of the eticlopride binding site showing the protein-ligand interaction. (B) Chemical structure of eticlopride and interactions with the D3R residues; hydrophobic contacts are shown in gray dashed lines, hydrogen bonds in blue, and salt bridges in red. The ligand binding sites in (C) D3R, (D) β2AR (PDB ID: 2RH1), and (E) A2AAR (PDB ID: 3EML) crystal structures are shown in exactly the same orientation. A semitransparent skin shows the molecular surface of the receptor, colored by the residue properties (green, hydrophobic; red, acidic; and blue, basic). Corresponding ligands (C) eticlopride, (D) carazolol, and (E) ZM241385 are shown with carbon atoms colored magenta. For the D3R pocket, residues conserved between D3R and β2AR are colored turquoise, and nonconserved residues are in gray.

 

Figure 4
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Fig. 4. The second binding pocket defined by R-22 is differentially modulated by nonconserved residues in D3R and D2R. (A) In addition to the core binding pocket, which essentially overlaps with that of eticlopride, the potential docking conformations of the core-constrained (see supporting online material) D3R-selective compound R-22 position the extended aryl amide within a second binding pocket comprising the junction of ECL1 and ECL2 and the interface of helices II, VII and I [dotted orange ellipse in (A)]. (B) In the docking pose with the most extended conformation of R-22 (yellow), the ligand makes contact with several key conserved residues, including Asp1103.32, Tyr3737.43, and Glu902.65. The linker region of R-22 connecting the aryl amide and phenylpiperazine moieties (see fig. S1) is in a thinner representation. The 2,3-diCl-phenylpiperazine occupies essentially the same space as bound eticlopride (orange). (C and D) Close-up view of the interface of helices II, VII, and I of the D3R (C) and D2R (D) showing the results of molecular dynamics simulations indicating that the nonconserved regions of helix I and position 7.38 (orange) may orient key conserved contact residues differently and alter the shape of the second binding pocket, as reflected by the simulated distances between Glu902.65 and Tyr3737.43 in D3R (cyan) and D2R (magenta) (see fig. S7).

 


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