NPASS Natural Product

Natural Product: NPC131479

Natural Product ID:	NPC131479
Common Name:	Ginsenoside F3
IUPAC Name:	(2S,3R,4S,5S,6R)-2-[(2S)-6-methyl-2-[(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-3,6,12-trihydroxy-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]hept-5-en-2-yl]oxy-6-[[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxymethyl]oxane-3,4,5-triol
Synonyms:	Ginsenoside F3
Molecular Formula:	C41H70O13
Standard InCHIKey:	HJRVLGWTJSLQIG-ABNMXWHVSA-N
Standard InCHI:	InChI=1S/C41H70O13/c1-20(2)10-9-13-41(8,54-36-33(50)31(48)30(47)25(53-36)19-52-35-32(49)29(46)24(44)18-51-35)21-11-15-39(6)28(21)22(42)16-26-38(5)14-12-27(45)37(3,4)34(38)23(43)17-40(26,39)7/h10,21-36,42-50H,9,11-19H2,1-8H3/t21-,22+,23-,24-,25+,26+,27-,28-,29-,30+,31-,32+,33+,34-,35-,36-,38+,39+,40+,41-/m0/s1
Canonical SMILES:	CC(=CCC[C@@]([C@H]1CC[C@@]2([C@@H]1[C@H](O)C[C@H]1[C@@]2(C)C[C@@H]([C@@H]2[C@]1(C)CC[C@@H](C2(C)C)O)O)C)(O[C@@H]1O[C@H](CO[C@@H]2OC[C@@H]([C@@H]([C@H]2O)O)O)[C@H]([C@@H]([C@H]1O)O)O)C)C
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
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	leaves and stems	PMID[25442304]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota		TM-MC*
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota		TM-MC*
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota		TM-MC*

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Biological Activity

Activity Type	# Activity
IC50	2
Others	2

Activity Type	# Activity
Cell Line	2
Individual Protein	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1044	Individual Protein	DNA topoisomerase II alpha	Homo sapiens	IC50	>	250000	nM	20371180
NPT143	Individual Protein	DNA topoisomerase I	Homo sapiens	IC50	>	250000	nM	20371180
NPT75	Cell Line	U251	Homo sapiens	Activity	=	103.91	%	25442304
NPT76	Cell Line	C6	Rattus norvegicus	Activity	=	93.57	%	25442304

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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 NPC131479 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	155
0.1-0.2	1125
0.2-0.3	3481
0.3-0.4	8013
0.4-0.5	8166
0.5-0.6	4424
0.6-0.7	3177
0.7-0.8	1453
0.8-0.85	548
0.85-0.9	228
0.9-0.95	59
0.95-1	60

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Similarity Score	Similarity Level	Natural Product ID
0.875	High Similarity	NPC285253
0.875	High Similarity	NPC475550
0.875	High Similarity	NPC224098
0.875	High Similarity	NPC150372
0.875	High Similarity	NPC249265

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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 NPC131479 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	165
0.1-0.2	1577
0.2-0.3	4123
0.3-0.4	2225
0.4-0.5	589
0.5-0.6	270
0.6-0.7	174
0.7-0.8	25
0.8-0.85	5
0.85-0.9	8
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6058	Remote Similarity	NPD6697	Approved
0.6063	Remote Similarity	NPD7100	Approved
0.6063	Remote Similarity	NPD7101	Approved
0.6066	Remote Similarity	NPD5247	Approved
0.6066	Remote Similarity	NPD5248	Approved

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Structure

CID131479 OpenBabel06191715492D 54 59 0 0 1 0 0 0 0 0999 V2000 -1.6752 -3.3488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1752 -2.4828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3510 1.4452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3729 1.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3150 -1.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4655 0.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0856 0.4441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0413 -2.9828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8248 -4.2148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1752 -4.2148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7315 -0.7032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2171 -0.9453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3248 -3.3488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2661 -1.2543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0117 -0.0341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3640 -1.8723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0366 0.7531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0209 2.5172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4228 1.0172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6752 -3.3488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3248 -1.6167 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4129 -2.1813 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9877 1.0621 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0209 3.5172 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5568 0.5172 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5719 -0.8942 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4250 0.0329 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6698 -1.5122 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1549 4.0172 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6908 1.0172 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8248 0.5172 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2889 3.5172 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8248 -0.4828 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7308 0.3930 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2889 2.5172 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6908 -0.9828 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6819 0.7020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5229 -0.5851 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8777 -0.5341 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8287 -0.2250 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8248 -2.4828 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2050 -3.1595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1956 2.0403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8869 4.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3761 0.3419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1549 5.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 2.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0413 1.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4228 4.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0413 -0.9828 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1549 2.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4228 2.0172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5568 -0.4828 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 -1.9828 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 1 0 0 0 0 2 20 1 0 0 0 0 3 37 1 0 0 0 0 4 37 1 0 0 0 0 6 39 1 0 0 0 0 9 10 1 0 0 0 0 9 13 1 0 0 0 0 10 20 2 0 0 0 0 11 15 1 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 27 1 0 0 0 0 13 41 1 0 0 0 0 14 38 1 0 0 0 0 15 39 1 0 0 0 0 16 22 1 0 0 0 0 16 26 1 0 0 0 0 17 23 1 0 0 0 0 17 40 1 0 0 0 0 18 24 1 0 0 0 0 18 51 1 0 0 0 0 19 52 1 0 0 0 0 21 28 1 0 0 0 0 21 41 1 6 0 0 0 22 28 1 0 0 0 0 22 42 1 6 0 0 0 23 34 1 0 0 0 0 23 43 1 1 0 0 0 24 29 1 0 0 0 0 24 44 1 1 0 0 0 25 19 1 1 0 0 0 25 30 1 0 0 0 0 25 53 1 0 0 0 0 26 38 1 6 0 0 0 26 40 1 0 0 0 0 27 37 1 0 0 0 0 27 45 1 6 0 0 0 28 39 1 1 0 0 0 29 32 1 0 0 0 0 29 46 1 1 0 0 0 30 31 1 0 0 0 0 30 47 1 6 0 0 0 31 33 1 0 0 0 0 31 48 1 1 0 0 0 32 35 1 0 0 0 0 32 49 1 6 0 0 0 33 36 1 0 0 0 0 33 50 1 6 0 0 0 34 37 1 0 0 0 0 34 38 1 6 0 0 0 35 51 1 0 0 0 0 35 52 1 1 0 0 0 36 53 1 0 0 0 0 36 54 1 1 0 0 0 38 5 1 6 0 0 0 39 40 1 6 0 0 0 40 7 1 6 0 0 0 41 8 1 6 0 0 0 41 54 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	46887678
ChEMBL	CHEMBL1095004
ZINC

Physicochemical Properties

Molecular Weight:	770.48
ALogP:	-1.2145
MLogP:	4.54
XLogP:	3.687
# Rotatable Bonds:	26
Polar Surface Area:	218.99
# H-Bond Aceptor:	13
# H-Bond Donor:	9
# Rings:	6
# Heavy Atoms:	54

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