NPASS Natural Product

Natural Product: NPC120123

Natural Product ID:	NPC120123
Common Name:	(2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-4,5-Dihydroxy-2-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-12-Hydroxy-17-[(2S)-2-Hydroxy-6-Methylhept-5-En-2-Yl]-4,4,8,10,14-Pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-Dodecahydro-1H-Cyclopenta[A]Phenanthren-3-Yl]Oxy]-6-(Hydroxymethyl)Oxan-3-Yl]Oxy-6-(Hydroxymethyl)Oxane-3,4,5-Triol
IUPAC Name:	(2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-2-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-12-hydroxy-17-[(2S)-2-hydroxy-6-methylhept-5-en-2-yl]-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]-6-(hydroxymethyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:	20(S)-Ginsenoside Rg3
Molecular Formula:	C42H72O13
Standard InCHIKey:	RWXIFXNRCLMQCD-JBVRGBGGSA-N
Standard InCHI:	InChI=1S/C42H72O13/c1-21(2)10-9-14-42(8,51)22-11-16-41(7)29(22)23(45)18-27-39(5)15-13-28(38(3,4)26(39)12-17-40(27,41)6)54-37-35(33(49)31(47)25(20-44)53-37)55-36-34(50)32(48)30(46)24(19-43)52-36/h10,22-37,43-51H,9,11-20H2,1-8H3/t22-,23+,24+,25+,26-,27+,28-,29-,30+,31+,32-,33-,34+,35+,36-,37-,39-,40+,41+,42-/m0/s1
Canonical SMILES:	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3C[C@@H](O)[C@H]3[C@@]2(C)CC[C@@H]3[C@](CCC=C(C)C)(O)C)C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)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
NPO10946	Scedosporium boydii	Species	Microascaceae	Eukaryota		UNPD*
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota		UNPD*
NPO12450	Cneorum pulverulentum	Species	Rutaceae	Eukaryota		UNPD*
NPO16669	Diospyros verrucosa	Species	Ebenaceae	Eukaryota		UNPD*
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria		UNPD*
NPO20395	Athanasia crithmifolia	Species	Asteraceae	Eukaryota		UNPD*
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	leaves and stems	PMID[25442304]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota		TM-MC*
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota		TCMID*
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota		TM-MC*

Showing 1 to 10 of 49 entries

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Biological Activity

Activity Type	# Activity
IC50	6
Others	9
Potency	5

Activity Type	# Activity
Cell Line	4
Individual Protein	5
Others	11

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1	Others	Radical scavenging activity		Inhibition	=	20	%	16901695
NPT1	Others	Radical scavenging activity		IC50	=	440000	nM	16901695
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
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	FC	=	2		21956953
NPT2	Others	Unspecified		Activity	=	16.1	%	17663584
NPT2	Others	Unspecified		Activity	=	35.9	%	17663584
NPT2	Others	Unspecified		Activity	=	140	%	17663584
NPT2	Others	Unspecified		Potency		10322.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency		7079.5	nM	PubChem BioAssay data set

Showing 1 to 10 of 20 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 NPC120123 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

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 NPC120123 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

Showing 1 to 5 of 200 entries

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Structure

CID120123 OpenBabel06191715472D 55 60 0 0 1 0 0 0 0 0999 V2000 -8.4352 3.6773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7012 4.8172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3600 0.6236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3436 0.6236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7037 3.9344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1110 1.9672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8591 2.5441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2941 6.6278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1188 5.1392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0809 5.3437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7728 3.9344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5555 1.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.9508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4607 5.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8518 3.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1946 3.1387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4073 1.9672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5555 4.4262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2591 -2.4590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8518 -1.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7391 4.6127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1946 4.7302 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4073 4.9180 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2591 -1.4754 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.9836 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7037 1.9672 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5555 3.4426 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 1.9672 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2591 4.4262 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1110 -0.9836 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8518 -1.4754 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1110 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7037 -0.9836 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2591 0.4918 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7037 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4073 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8518 0.4918 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8518 1.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7037 2.9508 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4073 2.9508 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2591 3.4426 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4986 5.6656 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1110 -2.9508 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7037 -0.9836 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4073 5.9016 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9628 -1.4754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8518 -2.4590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9628 0.4918 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5555 -1.4754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2591 1.4754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5631 5.9696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4073 -0.9836 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 0.8518 1.4754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5555 0.4918 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 21 1 0 0 0 0 3 38 1 0 0 0 0 4 38 1 0 0 0 0 6 40 1 0 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 21 2 0 0 0 0 11 16 1 0 0 0 0 11 22 1 0 0 0 0 12 17 1 0 0 0 0 12 26 1 0 0 0 0 13 15 1 0 0 0 0 13 28 1 0 0 0 0 14 42 1 0 0 0 0 15 39 1 0 0 0 0 16 41 1 0 0 0 0 17 40 1 0 0 0 0 18 23 1 0 0 0 0 18 27 1 0 0 0 0 19 43 1 0 0 0 0 20 44 1 0 0 0 0 22 29 1 0 0 0 0 22 42 1 6 0 0 0 23 29 1 0 0 0 0 23 45 1 6 0 0 0 24 19 1 1 0 0 0 24 30 1 0 0 0 0 24 52 1 0 0 0 0 25 20 1 1 0 0 0 25 31 1 0 0 0 0 25 53 1 0 0 0 0 26 38 1 0 0 0 0 26 39 1 6 0 0 0 27 39 1 6 0 0 0 27 40 1 0 0 0 0 28 38 1 0 0 0 0 28 54 1 6 0 0 0 29 41 1 1 0 0 0 30 32 1 0 0 0 0 30 46 1 6 0 0 0 31 33 1 0 0 0 0 31 47 1 6 0 0 0 32 34 1 0 0 0 0 32 48 1 1 0 0 0 33 35 1 0 0 0 0 33 49 1 1 0 0 0 34 36 1 0 0 0 0 34 50 1 6 0 0 0 35 37 1 0 0 0 0 35 55 1 6 0 0 0 36 52 1 0 0 0 0 36 55 1 1 0 0 0 37 53 1 0 0 0 0 37 54 1 1 0 0 0 39 5 1 6 0 0 0 40 41 1 1 0 0 0 41 7 1 1 0 0 0 42 8 1 1 0 0 0 42 51 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	9918693
ChEMBL	CHEMBL398412
ZINC

Physicochemical Properties

Molecular Weight:	784.50
ALogP:	-0.9589
MLogP:	4.65
XLogP:	5.318
# Rotatable Bonds:	27
Polar Surface Area:	218.99
# H-Bond Aceptor:	13
# H-Bond Donor:	9
# Rings:	6
# Heavy Atoms:	55

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