BioSimDB
Published June 2025 | Version v1
Dataset Open

P2Y1 purinergic receptor in the presence of 10% of phenol (PHX) 40 ns

Creators

  • 1. Queens University Belfast

Description

Probe MD simulations. Mapping an allosteric site at the lipid interface of the P2Y1 purinergic receptor. The P2Y1 receptor in the presence of 10% of phenol (PHX) in the water-POPC bilayer. 0.15M of Na+ and Cl-. Three replicates are provided.

Trajectory originally donated to SlimMD

Files

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Additional details

Identifiers

DOI
10.1021/acscentsci.1c00802

Domain Specific Metadata

 
Property Value
Software NAMD
Software Version Git-2017-12-19
Molecular Model atomistic
Simulation Method classical
Timestep 2 femtoseconds
Framestep 0.2 nanoseconds
Length 0.04 microseconds
Temperature 310 K
Pressure 1.01325 bar
Ensemble NPT
Box Type cubic
Trajectories Cartesian coordinates
Force Fields CHARMM36, CgenFF v1.0.0
Experimental Structures https://www.rcsb.org/structure/4XNV
Membrane Yes
Ligands https://pubchem.ncbi.nlm.nih.gov/compound/Phenol
Sequences SFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKDLDNSPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVDPILYFLAGDTFRRR
Box Dimensions 81.1 x 75.3 x 175.9 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees
Long Range Cutoff 12 Angstrom
Thermostat langevin
Barostat langevin
Atom Count 109703