NPASS Natural Product

Natural Product: NPC125039

Natural Product ID:	NPC125039
Common Name:	Silibinin
IUPAC Name:	3,5,7-trihydroxy-2-[3-(4-hydroxy-3-methoxyphenyl)-2-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-2,3-dihydrochromen-4-one
Synonyms:	Silibinin; Silymarin
Molecular Formula:	C25H22O10
Standard InCHIKey:	SEBFKMXJBCUCAI-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H22O10/c1-32-17-6-11(2-4-14(17)28)24-20(10-26)33-16-5-3-12(7-18(16)34-24)25-23(31)22(30)21-15(29)8-13(27)9-19(21)35-25/h2-9,20,23-29,31H,10H2,1H3
Canonical SMILES:	OCC1Oc2ccc(cc2OC1c1ccc(c(c1)OC)O)C1Oc2cc(O)cc(c2C(=O)C1O)O
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Reference
NPO17823	Lycium chinense	Species	Solanaceae	Eukaryota	fruits	PMID[12467621]
NPO21361	Anastatica hierochuntica	Species	Brassicaceae	Eukaryota		PMID[12643908]
NPO21361	Anastatica hierochuntica	Species	Brassicaceae	Eukaryota		PMID[20189399]
NPO5645	Silybum marianum	Species	Asteraceae	Eukaryota		TM-MC*

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Biological Activity

Activity Type	# Activity
AC50	4
EC50	5
IC50	30
Kd	2
Ki	18
MIC	3
Others	144
Potency	110

Activity Type	# Activity
Cell Line	73
Individual Protein	114
Organism	36
Others	89
Protein Family	1
Subcellular	1
Tissue	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1	Others	Radical scavenging activity		Activity	=	24.6	ug/ml	8594153
NPT1	Others	Radical scavenging activity		Activity	=	16.6	%	19660956
NPT1	Others	Radical scavenging activity		IC50	=	2100000	nM	20036447
NPT1	Others	Radical scavenging activity		IC50	=	284000	nM	22503365
NPT1	Others	Radical scavenging activity		IC50	=	392200	nM	25442301
NPT10	Individual Protein	Geminin	Homo sapiens	Potency		25929	nM	PubChem BioAssay data set
NPT10	Individual Protein	Geminin	Homo sapiens	Potency		206	nM	PubChem BioAssay data set
NPT100	Individual Protein	Glutaminase kidney isoform, mitochondrial	Homo sapiens	Potency		35481.3	nM	PubChem BioAssay data set
NPT102	Individual Protein	Interleukin-8	Homo sapiens	Potency		66824.2	nM	PubChem BioAssay data set
NPT103	Individual Protein	Nuclear receptor ROR-gamma	Homo sapiens	Potency		18833.6	nM	PubChem BioAssay data set

Showing 1 to 10 of 291 entries

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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 NPC125039 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	333
0.1-0.2	1201
0.2-0.3	2501
0.3-0.4	6036
0.4-0.5	6745
0.5-0.6	2878
0.6-0.7	3415
0.7-0.8	4189
0.8-0.85	1780
0.85-0.9	1246
0.9-0.95	533
0.95-1	32

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Similarity Score	Similarity Level	Natural Product ID
0.9172	High Similarity	NPC192083
0.9172	High Similarity	NPC213896
0.9172	High Similarity	NPC141212
0.9172	High Similarity	NPC58382
0.9172	High Similarity	NPC162351

Showing 1 to 5 of 200 entries

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Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC125039 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	334
0.1-0.2	859
0.2-0.3	1652
0.3-0.4	2624
0.4-0.5	1925
0.5-0.6	1072
0.6-0.7	503
0.7-0.8	140
0.8-0.85	24
0.85-0.9	17
0.9-0.95	8
0.95-1	3

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6975	Remote Similarity	NPD2861	Phase 2
0.6977	Remote Similarity	NPD7213	Phase 3
0.6977	Remote Similarity	NPD7212	Phase 2
0.6982	Remote Similarity	NPD2424	Discontinued
0.6987	Remote Similarity	NPD1548	Phase 1

Showing 1 to 5 of 200 entries

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Structure

CID125039 OpenBabel06191715482D 35 39 0 0 1 0 0 0 0 0999 V2000 8.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 32 1 0 0 0 0 2 4 2 0 0 0 0 2 11 1 0 0 0 0 3 5 2 0 0 0 0 3 12 1 0 0 0 0 4 14 1 0 0 0 0 5 16 1 0 0 0 0 6 11 2 0 0 0 0 6 17 1 0 0 0 0 7 12 2 0 0 0 0 7 18 1 0 0 0 0 8 13 2 0 0 0 0 8 15 1 0 0 0 0 9 13 1 0 0 0 0 9 19 2 0 0 0 0 10 20 1 0 0 0 0 10 26 1 0 0 0 0 11 24 1 0 0 0 0 12 25 1 0 0 0 0 13 27 1 0 0 0 0 14 17 2 0 0 0 0 14 28 1 0 0 0 0 15 21 2 0 0 0 0 15 29 1 0 0 0 0 16 18 2 0 0 0 0 16 33 1 0 0 0 0 17 32 1 0 0 0 0 18 34 1 0 0 0 0 19 21 1 0 0 0 0 19 35 1 0 0 0 0 20 24 1 0 0 0 0 20 33 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 30 2 0 0 0 0 23 25 1 0 0 0 0 23 31 1 0 0 0 0 24 34 1 0 0 0 0 25 35 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	5213
ChEMBL	CHEMBL1401508
ZINC

Physicochemical Properties

Molecular Weight:	482.12
ALogP:	-3.3761
MLogP:	3.11
XLogP:	0.66
# Rotatable Bonds:	10
Polar Surface Area:	155.14
# H-Bond Aceptor:	3
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	35

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