Published June 2025
| Version v1
Dataset
Open
P2Y1 purinergic receptor bound to BPTU the allosteric modulator 40 ns
Description
Classical MD simulations of the P2Y1 receptor bound to BPTU 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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Files
(785.2 MB)
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md5:35542381e69d6abd30d4f77f4634161d
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252.5 MB | Download |
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md5:987aa9eda7e28dac643fa9a90cafb69f
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252.5 MB | Download |
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md5:55e1d7d0ded4d503ff76b8bd78ce69e7
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252.5 MB | Download |
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md5:1538909fd792079d54c7aae16062ce51
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1.4 MB | Preview Download |
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md5:724a21006930a5cc177f9fb5ea6048a8
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8.3 MB | Download |
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md5:c90203652c2aacbb29043b58021dd51a
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18.0 MB | Download |
Additional details
Identifiers
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/bptu |
| Sequences | SFKCALTKTGFQFYYLPAVYILVFIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGDAMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVVAISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIVRALIYKDLDNSPLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGLASLNSCVDPILYFLAGDTFRRR |
| Box Dimensions | 76.2 x 77.8 x 169.2 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees |
| Long Range Cutoff | 12 Angstrom |
| Thermostat | langevin |
| Barostat | langevin |
| Atom Count | 105188 |