Ligand ID: RIO


Drugbank ID:
DB03615
(Ribostamycin)


Indication:
A broad-spectrum antimicrobial isolated from Streptomyces ribosifidicus. Ribostamycin, along with other aminoglycosides with the DOS (2-deoxystreptamine) subunit, is an important broad-spectrum antibiotic with important use against human immunodeficiency virus and is considered a critically important antimicrobial by the World Health Organization.

Get human targets for RIO in PDB (known and potential targets)

RESULTS FROM SUB-STRUCTURAL SIMILARITY SEARCHES MAPPED TO LIGAND 'RIO' AND SARS-COV-2 / COVID-19 STRUCTURES

1) User may click on the DrReposER ID (the first column) to get information on the binding sites and drug molecule.
2) Click View (the second last column) to view matched residues and superposition in the NGL viewer (upper right part).
3) User may also click on the Dock (the last column) to get script for molecular docking in UCSF Chimera throuh AutoDock Vina.

DrReposER ID / Desc. Hit
PDBID		 Hit
Macromolecule		 Res.
Matches		 View Interface RMSD Seq.
Identity (%)		 HETATM Dock
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		6vww URIDYLATE-SPECIFIC
ENDORIBONUCLEASE
(SARS-CoV-2)		4 / 8
VAL B 128
ARG B  62
HIS B  15
ASP B 125
1.62A19.05
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_B_RIOB501_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6vxx SPIKE GLYCOPROTEIN
(SARS-CoV-2)		5 / 9
GLU A 191
GLY A  35
SER A  31
ASP A 215
THR A  29
1.71A8.70
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_B_RIOB501_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6vyb SPIKE GLYCOPROTEIN
(SARS-CoV-2)		5 / 9
GLU A 191
GLY A  35
SER A  60
ASP A 215
THR A  29
1.41A8.70
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_A_RIOA500_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6w4h NSP16
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.67A20.25
None
ACT  A7104 (-3.4A)
None
ACT  A7104 ( 4.8A)
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_B_RIOB501_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6w4h NSP16
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.62A20.25
None
ACT  A7104 (-3.4A)
None
ACT  A7104 ( 4.8A)
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_B_RIOB501_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6w61 2'-O-METHYLTRANSFERA
SE
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.54A
None
EDO  A7102 (-3.2A)
None
EDO  A7102 ( 4.7A)
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_A_RIOA500_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6w61 2'-O-METHYLTRANSFERA
SE
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.58A
None
EDO  A7102 (-3.2A)
None
EDO  A7102 ( 4.7A)
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		6wlc URIDYLATE-SPECIFIC
ENDORIBONUCLEASE
(SARS-CoV-2)		4 / 8
VAL B 128
ARG B  62
HIS B  15
ASP B 125
1.62A17.51
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_A_RIOA500_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6wq3 2'-O-METHYLTRANSFERA
SE
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.63A
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1M4G_B_RIOB501_0
(AMINOGLYCOSIDE
2'-N-ACETYLTRANSFERA
SE)		6wq3 2'-O-METHYLTRANSFERA
SE
(SARS-CoV-2)		5 / 9
GLU A6945
GLY A6946
SER A6943
SER A6973
ASP A6977
1.58A
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		6ywk NSP3 MACRODOMAIN
(SARS-CoV-2)		4 / 8
TYR B 113
VAL B 151
ARG B 141
HIS B 138
1.64A21.28
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		6ywk NSP3 MACRODOMAIN
(SARS-CoV-2)		4 / 8
TYR B 113
VAL B 155
ARG B 141
HIS B 138
1.71A21.28
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
2BUE_A_RIOA1201_0
(AAC(6')-IB)		6ywl NSP3 MACRODOMAIN
(SARS-CoV-2)		5 / 11
GLY B  73
GLU E 170
SER E 167
ASP B  66
ASP E 135
1.80A24.64
None
None
None
None
EDO  B 202 (-4.8A)
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		6ywl NSP3 MACRODOMAIN
(SARS-CoV-2)		4 / 8
TYR B 113
VAL B 151
ARG B 141
HIS B 138
1.72A21.28
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		7btf NSP12
(SARS-CoV-2)		4 / 8
GLU A 658
VAL A 662
HIS A 642
ASP A 684
1.35A10.38
None
None
ZN  A1002 (-3.3A)
None
Potential target for repurposing, i.e. matched protein structure has less than 30% sequence identity to known drug target, and may potentially interact with the same drug molecule based on local structural similarity of binding site.
1S3Z_B_RIOB501_0
(AMINOGLYCOSIDE
6'-N-ACETYLTRANSFERA
SE)		7bv1 NSP12
NSP8
(SARS-CoV-2)		4 / 8
TYR A 674
VAL B 131
ARG A 624
ASP A 390
1.79A10.48
None