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Published June 2025 | Version v1
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Human dopamine transporter embedded in a membrane, bound to novel psychoactive substance MAPB 250ns

Creators

  • 1. University of Roehampton

Description

A trio of trajectories are supplied whose data was published in Sahai, M.A. et. al. 2017. They include the human dopamine transporter (hDAT), imbedded in a membrane, bound to amphetamine, MDMA and the new psychoactive substance (NPS) 5-MAPB. In VMD the segid for these compounds are AMP, MDMA and MAPB, respectively, If you align all three trajectories on the protein backbone they can be compared with respect to destabilisation of the second sodium NA2 in the binding site. Residues of importance can be found in Fig 5 and 6 of the attached paper. Any questions please direct them to Michelle Sahai: michelle.sahai@roehampton.ac.uk

Monovalent neutralising ionic environment.

Trajectory originally donated to SlimMD

Files

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md5:35edcca894dc12a6fbd174ea369445fe
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md5:e77e3799074a67358e672245e8ee8e19
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md5:b6e1e7f59d5b72643e2ffcd844373cdd
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Additional details

Identifiers

DOI
10.1016/j.pnpbp.2016.11.004

Domain Specific Metadata

 
Property Value
Software ACEMD
Molecular Model atomistic
Simulation Method classical
Timestep 4 femtoseconds
Framestep 2.5 nanoseconds
Length 0.25 microseconds
Temperature 310 K
Ensemble NVT
Box Type cubic
Trajectories Cartesian coordinates
Force Fields CHARMM27 (protein), CHARMM36 (lipids), TIP3P (water)
Experimental Structures https://www.rcsb.org/structure/4M48
Membrane Yes
Ligands https://pubchem.ncbi.nlm.nih.gov/compound/102336592
Sequences MSKSKCSVGLMSSVVAPAKEPNAVGPKEVELILVKEQNGVQLTSSTLTNPRQSPVEAQDRETWGKKIDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYLLFMVIAGMPLFYMELALGQFNREGAAGVWKICPILKGVGFTVILISLYVGFFYNVIIAWALHYLFSSFTTELPWIHCNNSWNSPNCSDAHPGDSSGDSSGLNDTFGTTPAAEYFERGVLHLHQSHGIDDLGPPRWQLTACLVLVIVLLYFSLWKGVKTSGKVVWITATMPYVVLTALLLRGVTLPGAIDGIRAYLSVDFYRLCEASVWIDAATQVCFSLGVGFGVLIAFSSYNKFTNNCYRDAIVTTSINSLTSFSSGFVVFSFLGYMAQKHSVPIGDVAKDGPGLIFIIYPEAIATLPLSSAWAVVFFIMLLTLGIDSAMGGMESVITGLIDEFQLLHRHRELFTLFIVLATFLLSLFCVTNGGIYVFTLLDHFAAGTSILFGVLIEAIGVAWFYGVGQFSDDIQQMTGQRPSLYWRLCWKLVSPCFLLFVVVVSIVTFRPPHYGAYIFPDWANALGWVIATSSMAMVPIYAAYKFCSLPGSFREKLAYAIAPEKDRELVDRGEVRQFTLRHWLKV
Box Dimensions 97.7 x 99.9 x 153.1 Angstrom, alpha: 90.0, beta: 90.0, gamma: 90.0 degrees
Long Range Cutoff 12 Angstrom
Thermostat Langevin
Barostat N/A
Atom Count 46981