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Simulation report

Technical information

General information

Name: C-c chemokine receptor type 5 in complex with maravirocum

PDB id: 4MBS.A

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 (158 mM), Chloride (227 mM)

Number of molecules:

Water: 13734

POPC: 155

Chloride: 56

Sodium ion: 39

Maravirocum: 1

C-C chemokine receptor type 5: 1

Total number of atoms: 67047

Simulation details

Software and version: ACEMD, GPUGRID

Forcefield and version: CHARMM, 36m Feb 2016

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

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, et al.. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature methods 17 (8). doi: 10.1038/s41592-020-0884-y. (http://doi.org/10.1038/s41592-020-0884-y)



GPCRmd publication page: 1469

Simulation components

Ligands

Orthosteric ligand(s)

Maravirocum

(1 molecule)


Experimental Data:
Kd: 25.0 nM More details

Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Maravirocum (orthosteric lig.)

Specific State ID: 5052

(1 molecule)


Water

Specific State ID: 5019

(13734 molecules)

H2O


Sodium ion

Specific State ID: 5016

(39 molecules)

Na+


POPC

Specific State ID: 5018

(155 molecules)


Chloride

Specific State ID: 5017

(56 molecules)

Cl-


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