Simulation report
Technical information
General information
Name: C-c chemokine receptor type 2 in complex with mtmdxaiuendndl-rjsmdtjlsa-o
PDB id: 6GPX
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: Sodium ion (162 mM), Chloride (213 mM)
Number of molecules:
Water: 11999
POPC: 154
Chloride: 46
Sodium ion: 35
[(3~{s},4~{s})-3-methoxyoxan-4-yl]-[(1~{r},3~{s})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{h}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium: 1
C-C chemokine receptor type 2: 1
Total number of atoms: 61575
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
Aranda-Garcia, David and Stepniewski, Tomasz Maciej and Torrens-Fontanals, Mariona and Garcia-Recio, Adrian and Lopez-Balastegui, Marta and Medel-Lacruz, Brian and Morales-Pastor, Adrian and Peralta-Garcia, Alejandro and Dieguez-Eceolaza, Miguel and Sotillo-Nunez, David and Ding, Tianyi and Drabek, Matthaus and Jacquemard, Celien and Jakowiecki, Jakub and Jespers, Willem and Jimenez-Roses, Mireia and Jun-Yu-Lim, Victor and Nicoli, Alessandro and Orzel, Urszula and Shahraki, Aida and Tiemann, Johanna K. S. and Ledesma-Martin, Vicente and Nerin-Fonz, Francho and Suarez-Dou, Sergio and Canal, Oriol and Pandy-Szekeres, Gaspar and Mao, Jiafei and Gloriam, David E. and Kellenberger, Esther and Latek, Dorota and Guixa-Gonzalez, Ramon and Gutierrez-de-Teran, Hugo and Tikhonova, Irina G. and Hildebrand, Peter W. and Filizola, Marta and Babu, M. Madan and Di Pizio, Antonella and Filipek, Slawomir and Kolb, Peter and Cordomi, Arnau and Giorgino, Toni and Marti-Solano, Maria and Selent, Jana. 2025. Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways. Nature Communications 16 (1). doi: 10.1038/s41467-025-57034-y. (http://dx.doi.org/10.1038/s41467-025-57034-y)
Find a list of all simulations published in this paper: 1535
Simulation components
Ligands
Receptor
Mutations
No mutations found
Other molecules
[(3~{s},4~{s})-3-methoxyoxan-4-yl]-[(1~{r},3~{s})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{h}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium (orthosteric lig.)
Specific State ID: 5223(1 molecule)
