NPASS Natural Product

Natural Product: NPC284039

Natural Product ID:	NPC284039
Common Name:	Ligustrazine
IUPAC Name:	2,3,5,6-tetramethylpyrazine
Synonyms:	2,3,5,6-Tetramethyl-Pyrazine; 2,3,5,6-Tetramethylpyrazine; Ligustrazine; Tetramethylpyrazine
Molecular Formula:	C8H12N2
Standard InCHIKey:	FINHMKGKINIASC-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C8H12N2/c1-5-6(2)10-8(4)7(3)9-5/h1-4H3
Canonical SMILES:	Cc1nc(C)c(nc1C)C
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO3532	Tridentata marginata	NA	NA	NA	UNPD*
NPO27018	Cynomorium songaricum	Species	Cynomoriaceae	Eukaryota	TCMID*
NPO9241	Adiantum capillus-veneris	Species	Pteridaceae	Eukaryota	UNPD*
NPO28019	Oleum curcumae	NA	NA	NA	TCMID*
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	HerDing*
NPO15634	Radix smilacis	Species	Lymnaeidae	Eukaryota	TCMID*
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	PMID[24333010]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	TCMID*
NPO22470	Corynebacterium glutamicum	Species	Corynebacteriaceae	Bacteria	European Journal of Organic Chemistry,2010,2687-2695
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	TCMID*
NPO25209	Curcuma aromatica	Species	Zingiberaceae	Eukaryota	TCM_Taiwan*
NPO23448	Vinegar	NA	NA	NA	TCMID*
NPO25209	Curcuma aromatica	Species	Zingiberaceae	Eukaryota	HerDing*
NPO25209	Curcuma aromatica	Species	Zingiberaceae	Eukaryota	TCMID*
NPO28125	Ephedra equisetina	Species	Ephedraceae	Eukaryota	TCM_Taiwan*
NPO28125	Ephedra equisetina	Species	Ephedraceae	Eukaryota	TCMID*
NPO28125	Ephedra equisetina	Species	Ephedraceae	Eukaryota	HerDing*
NPO24124	Curcuma longa	Species	Zingiberaceae	Eukaryota	TCMID*
NPO30473	Ligusticum wallichii	Species	Apiaceae	Eukaryota	PMID[25841319]
NPO7308	Fraxinus quadrangulata	Species	Oleaceae	Eukaryota	UNPD*
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	TCM_Taiwan*
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	HerDing*
NPO25160	Goniothalamus borneensis	Species	Annonaceae	Eukaryota	UNPD*
NPO3251	Jacobaea maritima	Species	Asteraceae	Eukaryota	UNPD*
NPO23203	Sojae semen praeparatum	NA	NA	NA	TCMSP*
NPO5446	Campsis flos	Species	Bignoniaceae	Eukaryota	TCMSP*
NPO25951	Chuanxiong rhizoma	NA	NA	NA	TCMSP*
NPO17237	Ephedra herba	Species	Ephedraceae	Eukaryota	TCMSP*
NPO8381	Curculiginis rhizome	NA	NA	NA	TCMSP*
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	TM-MC*
NPO22033	Cnidium officinale	Species	Apiaceae	Eukaryota	TM-MC*
NPO28125	Ephedra equisetina	Species	Ephedraceae	Eukaryota	TM-MC*
NPO21507	Ephedra intermedia	Species	Ephedraceae	Eukaryota	TM-MC*
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	TM-MC*
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	TM-MC*
NPO8874	Glehnia littoralis	Species	Apiaceae	Eukaryota	TM-MC*
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	TM-MC*
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	TM-MC*
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	TM-MC*
NPO8650	Perilla frutescens	Species	Lamiaceae	Eukaryota	TM-MC*
NPO19048	Pinellia ternata	Species	Araceae	Eukaryota	TM-MC*
NPO6583	Clematis chinensis	Species	Ranunculaceae	Eukaryota	TCMID*

Biological Activity

Activity Type	# Activity
EC50	5
IC50	1
Others	29
Potency	2

Activity Type	# Activity
Cell Line	7
Organism	6
Others	23
Tissue	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3911	Cell Line	ECV-304	Homo sapiens	EC50	=	452000	nM	17383884
NPT2535	Tissue	Plasma	Oryctolagus cuniculus	Activity	=	7.86	%	17383884
NPT2	Others	Unspecified		Inhibition	=	6.6	%	18790647
NPT2	Others	Unspecified		Inhibition	=	9	%	18790647
NPT2	Others	Unspecified		Inhibition	=	36.2	%	18790647
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	71.2	%	18790647
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	50	%	18790647
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	46.3	%	18790647
NPT3911	Cell Line	ECV-304	Homo sapiens	EC50	=	154350	nM	19329327
NPT2	Others	Unspecified		Activity	=	7.86	%	19329327
NPT3911	Cell Line	ECV-304	Homo sapiens	Activity	=	22.08	%	21993151
NPT3911	Cell Line	ECV-304	Homo sapiens	Activity	=	42.75	%	21993151
NPT3911	Cell Line	ECV-304	Homo sapiens	Activity	=	12.71	%	21993151
NPT3911	Cell Line	ECV-304	Homo sapiens	Activity	=	10.4	%	21993151
NPT3911	Cell Line	ECV-304	Homo sapiens	EC50	=	600000	nM	21993151
NPT2	Others	Unspecified		Activity	=	58.4	%	22579617
NPT2	Others	Unspecified		Activity	=	42.9	%	22579617
NPT2	Others	Unspecified		EC50	=	600000	nM	10.1039/C3MD20352B
NPT2	Others	Unspecified		Activity	=	10.4	%	10.1039/C3MD20352B
NPT2	Others	Unspecified		Activity	=	12.7	%	10.1039/C3MD20352B
NPT2	Others	Unspecified		Activity	=	22.1	%	10.1039/C3MD20352B
NPT2	Others	Unspecified		Activity	=	42.8	%	10.1039/C3MD20352B
NPT2	Others	Unspecified		Potency		54427.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency		43619.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Inhibition	=	19.6	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Inhibition	=	15.3	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Inhibition	=	8.6	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Inhibition	=	3.4	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		IC50	=	265300	nM	10.1039/C4MD00022F
NPT2	Others	Unspecified		Activity	=	40.9	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Activity	=	22.1	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Activity	=	13.6	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		Activity	=	11.4	%	10.1039/C4MD00022F
NPT2	Others	Unspecified		EC50	=	83400	nM	10.1039/C4MD00022F
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	8	%	26786697
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	15	%	26786697
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	16.2	%	26786697

Similar Natural Products in NPASS

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC284039 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	11568
0.1-0.2	15597
0.2-0.3	2853
0.3-0.4	790
0.4-0.5	68
0.5-0.6	6
0.6-0.7	3
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC229
0.7714	Intermediate Similarity	NPC270637
0.7571	Intermediate Similarity	NPC204104
0.7324	Intermediate Similarity	NPC100312
0.679	Remote Similarity	NPC277608
0.679	Remote Similarity	NPC262236
0.675	Remote Similarity	NPC76536

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC284039 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	606
0.1-0.2	4239
0.2-0.3	3406
0.3-0.4	816
0.4-0.5	85
0.5-0.6	8
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD9394	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD9472	Phase 3
0.5862	Remote Similarity	NPD8835	Approved
0.5604	Remote Similarity	NPD9101	Discontinued

Structure

External Identifiers

PubChem CID	14296
ChEMBL	CHEMBL303697
ZINC

Physicochemical Properties

Molecular Weight:	136.10
ALogP:	1.758
MLogP:	2.12
XLogP:	1.992
# Rotatable Bonds:	4
Polar Surface Area:	25.78
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	10

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