4NTJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 4NTJ

Classification: MEMBRANE PROTEIN

Total Structure Weight: 55205.81

Macromolecule Entities
Molecule Chains Length Organism Details
P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12 A 466 Escherichia coli Homo sapiens Mutation: M1007W, H1102I, R1106L, D294N
Details: Chimera protein of N-terminal residues 2-223 from P2Y12R (P2Y12_HUMAN), Soluble cytochrome b562 (C562_ECOLX), and C-terminal residues 224-342 from P2Y12R (P2Y12_HUMAN).
Gene Name(s): cybC P2RY12 Gene View HORK3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: P2Y12 receptor in complex with an antithrombotic drug


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AZJ
Query on AZJ

A ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin- 1-yl}-5-cyano-2-methylpyridine-3-carboxylate
C23 H26 N4 O5 S
NEMHKCNXXRQYRF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLR
Query on CLR

A CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AZJ IC50: 9 - 3200 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.220
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 98.65 α = 90.00
b = 156.43 β = 111.08
c = 47.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-12-02
  • Released Date: 2014-03-26
  • Deposition author(s): Zhang, K., Zhang, J., Gao, Z.-G., Zhang, D., Zhu, L., Han, G.W., Moss, S.M., Paoletta, S., Kiselev, E., Lu, W., Fenalti, G., Zhang, W., Muller, C.E., Yang, H., Jiang, H., Cherezov, V., Katritch, V., Jacobson, K.A., Stevens, R.C., Wu, B., Zhao, Q., GPCR Network (GPCR)

Revision History

  • 2014-05-28
    Type: Database references
  • 2017-06-21
    Type: Database references, Source and taxonomy, Structure summary