Structure of the human P2Y12 receptor in complex with an antithrombotic drug

After the 2012 Nobel Prize in Chemistry was awarded for the study of G-protein-coupled receptors (GPCRs), renewed interest was evident within the field. As seven-transmem-brane (7TM) receptors with crucial physiological and pathological functions, GPCRs are the most popular drug targets known. In recent years, the Chinese government has funded several major projects on basic GPCR research and new drug discovery research targeting GPCRs through the National Basic Research Program (973 Program) and National Scientific and Technological Major Project for " Significant New Drugs Creation and Manufacturing Program ". With the support from 973 Program (2012CB910400), Dr. Zhao Qiang's group from the Shanghai Institute of Materia Medica reported the high resolution (2.7 Å) crystal structure of P2Y 12 R in complex with a non-nucleotide reversible antagonist , AZD1283, in Nature [1]. Their findings provide the ground work for P2Y 12 R-based drug research and development. Purinergic P2Y receptors which belong to the group of metabotropic P2Y purinergic GPCRs stimulated by nucleotides , play crucial roles in inflammation, cancer and cardio-vascular diseases. There are two distinct P2Y receptors for ADP expressed on platelets: the Gq-coupled P2Y 1 R and the Gi-coupled P2Y 12 R. Both contribute to collagen-induced platelet microparticle formation in whole blood and the formation of platelet-leukocyte aggregates. However, only P2Y 12 R is involved in the exposure of phosphatidylserine by thrombin or other platelet agonists [2]. P2Y 12 R (formerly SP1999) was discovered and identified as an ADP receptor with platelet clopidogrel sensitivity in 2001 [3]. Several generations of P2Y 12 R-targeted antithrombotic drugs have been developed because of its critical functional role in platelet aggregation. The first generation drugs, such as ticlopidine, clopidogrel and prasugrel, were prodrugs which needed to be metabolized before covalently binding to P2Y 12 R. Now newer drugs including ticagrelor, cangrelor and elinogrel that are either approved by the FDA or are still in clinical trials, directly act on P2Y 12 R. However, clinical studies have revealed certain limitations of these drugs including their long half-life and/or significant side effects. There is an unfulfilled medical need to develop new generation P2Y 12 R inhibitors, which was previously severely limited because of a lack of receptor structural and biochemical information. Dr. Zhao's group modified the protein sequence of the P2Y 12 R by inserting the thermostabilized apocytochrome b 562 RIL (BRIL) into the third intracellular loop region of the receptor, and incorporating a D294 7.49 …

The table below summarises the geometric issues observed across the polymeric chains and their t to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% The upper red bar (where present) indicates the fraction of residues that have poor t to the electron density. The numeric value is given above the bar.

Mol Chain Length
Quality of chain 1 A 466 The following table lists non-polymeric compounds, carbohydrate monomers and non-standard residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-t criteria: Mol Type Chain Res Chirality Geometry Clashes Electron density 4 OLC A 1204 ---X O There are 5 unique types of molecules in this entry. The entry contains 3025 atoms, of which 0 are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms.
Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 Residue-property plots i O These plots are drawn for all protein, RNA and DNA chains in the entry. The rst graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry and electron density. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor t to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey.

Mol Chain Bond lengths Bond angles
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers. The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 2.
All (15) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. There are no chirality outliers.
All (26) torsion outliers are listed below: Mol Chain Res Type Atoms There are no ring outliers.
3 monomers are involved in 4 short contacts: Mol The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths, bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the validation Tables will also be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles is within 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier. Any bond that is central to one or more torsion angles identied as an outlier by Mogul will be highlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ring in question and similar rings identied by Mogul is calculated over all ring torsion angles. If the average RMSD is greater than 60 degrees and the minimal RMSD between the ring in question and any Mogul-identied rings is also greater than 60 degrees, then that ring is considered an outlier. The outliers are highlighted in purple. The color gray indicates Mogul did not nd sucient equivalents in the CSD to analyse the geometry.

Ligand OLC A 1204
Bond lengths Bond angles The following is a graphical depiction of the model t to experimental electron density of all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the geometry validation Tables will also be included. Each t is shown from dierent orientation to approximate a three-dimensional view.
Electron density around OLC A 1204: