RMSD of submitted models. (A) Distribution of ligand RMSD (gold bars) and protein Cα RMSD (blue bars) for all models. (B) A scatterplot of ligand RMSD (y axis) versus binding site RMSD (x axis) for all models. The binding site RMSD values are calculated for heavy atoms of the binding site residues (F168^5.29, E169^5.30, M177^5.38, W246^6.48, L249^6.51, H250^6.52, N253^6.55, H264^6.66, M270^7.35) after the models are superimposed to the crystal structure using the protein Cα atoms.

Statistics of the two key receptor-ligand interactions in all models. (A) The hydrogen bonding interaction with N253^6.55 and the aromatic stacking interaction with F168^5.29 are shown by dashed lines with the distance measurements from the crystal structure. (B) Distribution of the distance for the interaction between the sidechain carbonyl oxygen OD1 atom in N253^6.55 and the exocyclic N15 atom of the ligand, and the average interatomic distance for the aromatic stacking interaction between the heavy atoms in the F168^5.29 sidechain and the bicyclic ring (atoms C11, N12, N13, C14, N15, N16, N17, C18, N19, C20) of ZM241385. (C) A scatterplot of the distances for the hydrogen bonding interaction (y axis) versus the aromatic stacking interaction (x axis).

Superposition of all 206 submitted models to the crystal structure of the human adenosine A_2A receptor (PDB ID: 3EML without the T4-lysozyme). Protein Cα atom superposition between model and crystal structure was done using the align command in PyMOL (version 1.0r2, www.pymol.org). The receptor is shown as two orthogonal views of Cα traces (A, B) with tube thickness being proportional to the RMSD about each Cα position clearly showing how well the TM regions were modeled and how much uncertainty are in the loop regions. (C) A superposition of stick diagrams of the ligand (ZM241385) from 169 models, a CPK model is used to delineate the observed position in the crystal structure. The C-terminus (residue numbers >306) is removed from all models.

Distribution of Cα RMSDs for TM helices I to VII (helix I: 6–34; helix II: 40–67; helix III: 73–107; helix IV: 117–142; helix V: 173–205; helix VI: 222–258; helix VII: 266–291), and the loop regions (ICL1: 35–39; ICL2: 108–116; ECL1: 68–72; ECL2:143–172 excluding 149–155 that are missing in the crystal structure; ECL3: 259–265).

A scatterplot of the number of correct contacts (y axis) versus ligand RMSD (x axis) for the best predictions from all groups. The best predictions from the top six groups are marked as gold crosses.

Comparison between the best models and the crystal structure around the ligand-binding site. (A) The ligand and the ligand-binding residues F168^5.29, E169^5.30, M177^5.38, L249^6.51, N253^6.55, H264^6.66 are shown for the best model (Costanzi) and the crystal structure. The ligand is shown as sticks for the model (magenta colored carbon atoms) and semitransparent spheres (green colored carbon atoms) for the crystal structure; the ligand-binding residues are shown as yellow sticks for the model, and blue sticks for the crystal structure. Extracellular (B) and side views (C) of the ligand in the binding pocket for the best predictions from the top six groups (magenta sticks for models, and green spheres for the crystal structure). The receptor crystal structure is in gray ribbons. The disulfide bonds are shown in orange sticks (D) The ligand-binding residues F168^5.29 and N253^6.55 are shown as sticks for the best predictions from the top six groups (yellow for models, and blue for the crystal structure). In (B), (C) and (D) the models are labeled as a – Constanzi; b - Katritch; c - Lam; d - Davis; e - Maigret; f – Jurkowski.