3VW7

Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom

Structural Biology Knowledgebase: 3VW7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VW7

Classification: Signaling protein / antagonist

Total Structure Weight: 58099.44

Macromolecule Entities
Molecule Chains Length Organism Details
Proteinase-activated receptor 1, Lysozyme A 484 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: N250G, N259S, D1020N, C1054T, C1097A
Details: Chimera protein of residues 86-395 form Proteinase-activated receptor 1 (P25116, PAR1_HUMAN), Lyzosyme from Enterobacteria phage T4 (P00720, LYS_BPT4) and residues 303-395 from Proteinase-activated receptor 1 (P25116, PAR1_HUMAN)
Gene Name(s): E F2R Gene View CF2R PAR1 TR

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VPX
Query on VPX

A ethyl [(1R,3aR,4aR,6R,8aR,9S,9aS)-9-{(E)- 2-[5-(3-fluorophenyl)pyridin-2-yl]ethenyl}- 1-methyl-3-oxododecahydronaphtho[2,3-c]furan- 6-yl]carbamate
vorapaxar (Synonym)
C29 H33 F N2 O4
ZBGXUVOIWDMMJE-QHNZEKIYSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VPX N/A in BindingDB
N/A in BindingMoad
Ki: 8 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.218
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 44.04 α = 90.00
b = 71.46 β = 90.00
c = 172.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-07
  • Released Date: 2012-12-12
  • Deposition author(s): Zhang, C., Srinivasan, Y., Arlow, D.H., Fung, J.J., Palmer, D., Zheng, Y., Green, H.F., Pandey, A., Dror, R.O., Shaw, D.E., Weis, W.I., Coughlin, S.R., Kobilka, B.K.

Revision History

  • 2013-08-14
    Type: Citation | Details: Citation update