Simulation report
Technical information
General information
Name: Glucagon-like peptide 1 receptor in complex with pptkuljudjwtsa-uhfffaoysa-n
PDB id: 5VEX
Activation state: Inactive
Description: Classical unbiased (NVT ensemble) complex flexibility assay.
Submitted by: GPCRmd community
System setup
Solvent type: TIP3P
Membrane type: Homogeneous
Membrane composition: POPC
Ionic composition: Chloride (174 mM), Sodium ion (157 mM)
Number of molecules:
Water: 26533
POPC: 327
Chloride: 83
Sodium ion: 75
4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-n-(1h-tetrazol-5-yl)benzamide: 1
Glucagon-like peptide 1 receptor: 1
Total number of atoms: 128732
Simulation details
Software and version: ACEMD3, GPUGRID
Forcefield and version: CHARMM, c36 Jul 2020
Time step : 4.0 fs
Delta : 0.2 ns
Replicates: 3
Accumulated simulation time: 1.5 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
David Aranda-García, Tomasz Maciej Stepniewski, Mariona Torrens-Fontanals, Adrian García-Recio, Marta Lopez-Balastegui, Brian Medel-Lacruz, Adrián Morales-Pastor, Alejandro Peralta-García, Miguel Dieguez-Eceolaza, David Sotillo-Nuñez, Tianyi Ding, Matthäus Drabek, Célien Jacquemard, Jakub Jakowiecki, Willem Jespers, Mireia Jiménez-Rosés, Víctor Jun-Yu-Lim, Alessandro Nicoli, Urszula Orzel, Aida Shahraki, Johanna K. S. Tiemann, Vicente Ledesma-Martin, Francho Nerín-Fonz, Sergio Suárez-Dou, Oriol Canal, Gáspár Pándy-Szekeres, Jiafei Mao, David E. Gloriam, Esther Kellenberger, Dorota Latek, Ramon Guixà-González, Hugo Gutiérrez-de-Terán, Irina G. Tikhonova, Peter W. Hildebrand, Marta Filizola, M. Madan Babu, Antonella Di Pizio, Slawomir Filipek, Peter Kolb, Arnau Cordomi, Toni Giorgino, Maria Marti-Solano, Jana Selent.. None. Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways. None. doi: 2ndround.
GPCRmd publication page: 1535
Simulation components
Ligands
(1 molecule)
Receptor
Mutations
No mutations found
Other molecules
4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-n-(1h-tetrazol-5-yl)benzamide (orthosteric lig.)
Specific State ID: 5258(1 molecule)
