NPASS Natural Product

Natural Product: NPC110656

Natural Product ID:	NPC110656
Common Name:	Saikosaponin-B3
IUPAC Name:	(2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-2-[[(3S,4R,4aR,6aR,6bS,8S,8aS,12aS,14R,14aR,14bS)-8-hydroxy-4,8a-bis(hydroxymethyl)-14-methoxy-4,6a,6b,11,11,14b-hexamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-3,5-dihydroxy-6-methyloxan-4-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:
Molecular Formula:	C43H72O14
Standard InCHIKey:	GLQYFMRUYWFXGT-ZGFARVGISA-N
Standard InCHI:	InChI=1S/C43H72O14/c1-21-29(48)34(57-36-32(51)31(50)30(49)25(18-44)55-36)33(52)37(54-21)56-28-10-11-39(4)26(40(28,5)19-45)9-12-41(6)35(39)24(53-8)15-22-23-16-38(2,3)13-14-43(23,20-46)27(47)17-42(22,41)7/h15,21,23-37,44-52H,9-14,16-20H2,1-8H3/t21-,23+,24-,25-,26-,27+,28+,29+,30-,31+,32-,33-,34+,35-,36+,37+,39+,40+,41-,42-,43-/m1/s1
Canonical SMILES:	CO[C@@H]1C=C2[C@@H]3CC(C)(C)CC[C@]3(CO)[C@H](C[C@]2([C@]2([C@H]1[C@@]1(C)CC[C@@H]([C@@]([C@@H]1CC2)(C)CO)O[C@@H]1O[C@H](C)[C@@H]([C@@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)C)C)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	Collection Location	Collection Time	Reference
NPO3107	Bupleurum falcatum	Species	Apiaceae	Eukaryota				TCM_Taiwan*

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Biological Activity

Activity Type	# Activity
IC50	5
Others	3

Activity Type	# Activity
Cell Line	7
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1872	Cell Line	Bcap37	Homo sapiens	IC50	>	80000	nM	26883148
NPT2	Others	Unspecified		IC50	>	80000	nM	26883148
NPT519	Cell Line	SH-SY5Y	Homo sapiens	Activity	=	63.12	%	26883148
NPT519	Cell Line	SH-SY5Y	Homo sapiens	Activity	=	8.25	%	26883148
NPT519	Cell Line	SH-SY5Y	Homo sapiens	Activity	=	6.16	%	26883148
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	27530	nM	26883148
NPT81	Cell Line	A549	Homo sapiens	IC50	>	80000	nM	26883148
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	64270	nM	26883148

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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 NPC110656 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	170
0.1-0.2	1100
0.2-0.3	3124
0.3-0.4	6015
0.4-0.5	9639
0.5-0.6	5516
0.6-0.7	3206
0.7-0.8	1279
0.8-0.85	556
0.85-0.9	233
0.9-0.95	45
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
0.8585	High Similarity	NPC476883
0.8586	High Similarity	NPC135224
0.8586	High Similarity	NPC100892
0.8586	High Similarity	NPC477969
0.8586	High Similarity	NPC477970

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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 NPC110656 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	1563
0.2-0.3	3864
0.3-0.4	2295
0.4-0.5	815
0.5-0.6	323
0.6-0.7	84
0.7-0.8	19
0.8-0.85	10
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5678	Remote Similarity	NPD4697	Phase 3
0.5679	Remote Similarity	NPD8470	Clinical (unspecified phase)
0.5682	Remote Similarity	NPD8444	Approved
0.5688	Remote Similarity	NPD6898	Phase 1
0.5691	Remote Similarity	NPD6008	Approved

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Structure

CID110656 OpenBabel06191715462D 57 63 0 0 1 0 0 0 0 0999 V2000 -8.5249 1.9687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1972 -3.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2128 -3.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5575 -0.4922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9022 2.8212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8525 1.4766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4100 -0.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7050 1.9687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2625 0.4922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4100 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8525 1.4766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5575 -2.4609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5575 -1.4766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8525 -1.4766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8525 -2.4609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8525 0.4922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2299 -0.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9178 2.8212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5575 -0.4922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6724 1.4766 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8525 -1.4766 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7050 -0.9844 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.3774 -1.4766 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5575 1.4766 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7050 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2625 1.4766 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.6724 0.4922 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.3774 -2.4609 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5249 -2.9531 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.6724 -2.4609 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9675 0.4922 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8200 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7050 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.6724 -1.4766 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9675 1.4766 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7050 -2.9531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5575 0.4922 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4100 1.9687 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8525 0.4922 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7050 -0.9844 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.0824 -1.4766 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9334 2.8212 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4100 -0.9844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5575 0.4922 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5249 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2299 -2.9531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5249 -3.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8200 -2.9531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1150 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5575 -1.4766 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8200 1.9687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5249 -0.9844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1150 1.9687 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8200 -0.9844 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 38 1 0 0 0 0 3 38 1 0 0 0 0 6 41 1 0 0 0 0 8 53 1 0 0 0 0 9 12 1 0 0 0 0 9 26 1 0 0 0 0 10 11 1 0 0 0 0 10 28 1 0 0 0 0 11 39 1 0 0 0 0 12 41 1 0 0 0 0 13 14 1 0 0 0 0 13 38 1 0 0 0 0 14 43 1 0 0 0 0 15 22 2 0 0 0 0 15 24 1 0 0 0 0 16 23 1 0 0 0 0 16 38 1 0 0 0 0 17 27 1 0 0 0 0 17 42 1 0 0 0 0 18 44 1 0 0 0 0 19 40 1 0 0 0 0 19 45 1 0 0 0 0 20 46 1 0 0 0 0 21 1 1 1 0 0 0 21 29 1 0 0 0 0 21 54 1 0 0 0 0 22 23 1 0 0 0 0 22 42 1 0 0 0 0 23 43 1 1 0 0 0 24 35 1 0 0 0 0 24 53 1 1 0 0 0 25 18 1 1 0 0 0 25 30 1 0 0 0 0 25 55 1 0 0 0 0 26 39 1 6 0 0 0 26 40 1 0 0 0 0 27 43 1 6 0 0 0 27 47 1 0 0 0 0 28 40 1 6 0 0 0 28 56 1 0 0 0 0 29 34 1 0 0 0 0 29 48 1 1 0 0 0 30 31 1 0 0 0 0 30 49 1 6 0 0 0 31 32 1 0 0 0 0 31 50 1 1 0 0 0 32 36 1 0 0 0 0 32 51 1 6 0 0 0 33 34 1 0 0 0 0 33 37 1 0 0 0 0 33 52 1 6 0 0 0 34 57 1 1 0 0 0 35 39 1 6 0 0 0 35 41 1 0 0 0 0 36 55 1 0 0 0 0 36 57 1 1 0 0 0 37 54 1 0 0 0 0 37 56 1 1 0 0 0 39 4 1 6 0 0 0 40 5 1 6 0 0 0 41 42 1 1 0 0 0 42 7 1 1 0 0 0 43 20 1 6 0 0 0 M END $$$$

External Identifiers

PubChem CID	21637635
ChEMBL	CHEMBL3794000
ZINC

Physicochemical Properties

Molecular Weight:	812.49
ALogP:	-2.9013
MLogP:	4.65
XLogP:	3.322
# Rotatable Bonds:	25
Polar Surface Area:	228.22
# H-Bond Aceptor:	14
# H-Bond Donor:	9
# Rings:	7
# Heavy Atoms:	57

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Structure MOL file
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