Naphthalene binding pocket

Cyanidin-3-O-glucoside

Code: 7JRN_C3OG

GRL-0617

Code: 7JRN_GRL; 7JRN_US_GRL

Hypericin

Code: 7JRN_HPCN; 7JRN_US_HPCN

Details

Cyanidin-3-O-glucoside (Gromacs 2018.2, force field: CHARMM27):

7JRN_C3OG-1: Cyanidin-3-O-glucoside bound to the naphthalene binding site of the papain-like protease (10 ns, 157780 atoms)

7JRN_C3OG-2: Cyanidin-3-O-glucoside bound to the naphthalene binding site of the papain-like protease (100 ns, 157780 atoms)

7JRN_C3OG-3: Cyanidin-3-O-glucoside bound to the naphthalene binding site of the papain-like protease  (100 ns, 157780 atoms)

7JRN_C3OG-4: Cyanidin-3-O-glucoside bound to the naphthalene binding site of the papain-like protease (100 ns, 157780 atoms)


GRL-0617 (Gromacs 2018.2, force field: CHARMM27): 

7JRN_GRL-1: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms) 

7JRN_GRL-2: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms) 

7JRN_GRL-3: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms) 

7JRN_GRL-4: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms) 

7JRN_GRL-5: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms) 

7JRN_GRL-6: GRL-0617 bound to the naphthalene binding site of the papain-like protease (100 ns, 157766 atoms)

7JRN_US_GRL:  GRL-0617 bound to the naphthalene binding site of the papain-like protease (1000 ns, 157766 atoms)


Hypericin (Gromacs 2018.2, force field: CHARMM27): 

7JRN_HPCN-1: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_HPCN-2: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_HPCN-3: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_HPCN-4: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_HPCN-5: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_HPCN-6: Hypericin bound to the naphthalene binding site of the papain-like protease (100 ns, 157777 atoms)

7JRN_US_HPCN: Hypericin bound to the naphthalene binding site of the papain-like protease (1000 ns, 157777 atoms)

Hypericin isomer

Code: 7JRN_HYPE; 7JRN_US_HYPE

Rutin

Code: 7JRN_RUTIN


Details

Hypericin isomer (Gromacs 2018.2, force field: CHARMM27): 

7JRN_HYPE-1: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (100 ns, 157783 atoms)

7JRN_HYPE-2: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (18 ns, 157783 atoms)

7JRN_HYPE-3: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (100 ns, 157783 atoms)

7JRN_HYPE-4: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (100 ns, 157783 atoms)

7JRN_HYPE-5: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (100 ns, 157783 atoms)

7JRN_HYPE-6: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (100 ns, 157783 atoms)

7JRN_US_HYPE: Hypericin isomer bound to the naphthalene binding site of the papain-like protease (1000 ns, 157783 atoms)


Rutin (Gromacs 2018.2, force field: CHARMM27): 

7JRN_RUTIN-1: Rutin bound to the naphthalene binding site of the papain-like protease (100 ns, 157760 atoms)

7JRN_RUTIN-2: Rutin bound to the naphthalene binding site of the papain-like protease (100 ns, 157760 atoms)

7JRN_RUTIN-3: Rutin bound to the naphthalene binding site of the papain-like protease (100 ns, 157760 atoms)