NPASS Compound

Natural Product: NPC203434

Natural Product ID	NPC203434
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ginsenoside R2
IUPAC Name	[(2R,3S,4S,5R,6R)-6-[[(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-3,12-dihydroxy-17-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-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-6-yl]oxy]-3,4-dihydroxy-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]methyl acetate
Synonyms	Ginsenoside R2; Vina-Ginsenoside R2
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL448234
PubChem CID	44593678
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 130136 0 0 0 0 0 0 0 0999 V2000 -7.0571 -0.4120 5.0216 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9587 0.1346 4.1509 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0294 1.3383 3.7889 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8834 -0.6137 3.7316 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8285 -0.1478 2.9160 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2997 0.3128 1.5434 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0329 -0.8605 0.9342 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6214 -0.4128 -0.3893 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5016 0.2378 -1.1495 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1779 0.2335 -0.5204 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4575 -0.9047 -0.3427 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1793 -0.8901 -0.7790 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1874 -0.9319 0.4199 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1867 -0.5913 -0.1376 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0856 0.7900 -0.6744 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5351 -1.6628 -1.1184 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9723 -1.5862 -1.5955 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8102 -1.8247 -0.3188 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6239 -0.5484 0.4288 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5077 -0.2094 1.5375 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5057 0.1699 2.6494 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2257 0.5246 1.8821 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1907 -0.6598 0.9683 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0492 -1.8592 1.8705 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5205 0.8774 1.3634 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8522 2.2323 1.0393 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5985 0.7120 0.3952 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8509 0.3929 1.1958 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4294 0.7048 2.5836 C 0 0 1 0 0 0 0 0 0 0 0 0 8.3709 1.7171 3.1816 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7874 1.2012 3.2322 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3629 3.0305 2.4602 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9581 1.9053 4.5206 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1406 1.1045 2.5818 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0655 -2.2537 -0.5696 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5671 -1.9526 -2.2117 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6900 -1.0498 -3.3962 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9409 -3.3547 -2.7146 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1777 -4.3312 -2.6733 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3851 -3.7638 -3.3283 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8637 -2.5745 -2.5293 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4738 -1.6230 -3.4777 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9688 -3.1333 -1.6150 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8155 -2.0568 -1.6164 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2055 -3.4768 -4.6847 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2973 0.8034 0.7723 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8712 1.6187 -1.2051 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1512 2.0507 -2.4696 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5385 2.7058 -2.4283 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5211 3.8440 -1.4684 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2146 4.0997 -0.7865 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0060 3.8810 -1.6605 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2699 3.0964 -2.7640 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2049 5.4718 -0.4330 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4729 3.5837 -0.4670 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8176 3.2184 -3.7172 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2862 -1.4141 -1.0610 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1187 -1.1519 1.7551 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0183 -0.2368 4.4850 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0734 0.1755 5.9649 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9060 -1.4821 5.1727 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1559 -1.0525 2.7876 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2121 0.6089 3.4280 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0471 1.1103 1.7054 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4295 -1.7833 0.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4347 0.3180 -0.0921 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5546 -0.1594 -2.1815 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5429 0.9857 -1.0618 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0024 0.0580 -1.3273 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4601 -0.1421 1.1292 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2931 -1.9011 0.8637 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7991 0.8842 -1.7403 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2061 1.2942 -0.1615 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9886 1.4276 -0.5799 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5353 -2.6226 -0.5076 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2004 -2.3282 -2.3562 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2713 -0.6073 -1.9674 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2810 -2.6380 0.2307 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5901 0.3428 -0.2472 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0308 -1.1180 1.8988 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8177 1.0597 3.1912 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3605 -0.6415 3.3657 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4152 1.4803 1.4071 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3917 0.5382 2.6129 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0355 -2.2772 2.2048 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5502 -1.5631 2.8433 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4657 -2.6869 1.4958 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2742 2.2111 0.1195 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3983 2.6899 1.9180 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7221 2.9228 0.7978 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5420 -0.0147 -0.3965 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8621 1.6835 -0.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7263 1.0094 0.8979 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1429 -0.6813 1.0606 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5578 -0.2249 3.1944 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3932 1.7245 4.0123 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3278 1.3501 2.2750 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8637 0.1168 3.4519 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8605 2.9414 1.4988 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3517 3.4891 2.4442 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0158 3.7181 3.0734 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6133 1.4870 5.1625 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4593 -2.6512 0.2213 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7239 -0.5926 -3.3403 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7662 -1.6168 -4.3758 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1087 -0.3349 -3.5544 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3168 -3.3234 -3.7739 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7864 -3.7990 -2.1464 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1387 -5.2120 -3.2783 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4473 -4.7268 -1.6859 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1609 -4.5818 -3.3301 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0649 -1.7780 -4.5151 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5733 -1.8691 -3.5808 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4487 -0.5574 -3.1951 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5585 -3.3554 -0.5874 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8684 -2.5138 -1.6109 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3200 -4.1417 -1.9780 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6822 -2.9073 -0.8526 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1751 -4.3449 -5.1605 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0681 1.3239 -3.2752 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2828 1.9263 -2.2409 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8916 4.7985 -1.9496 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1243 3.5678 0.1903 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2173 3.3688 -1.0317 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5469 4.8338 -1.9911 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9685 5.6454 0.1968 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4457 4.2537 0.2548 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2291 4.0172 -3.8947 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5060 -1.1700 -1.9809 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9164 -1.4672 1.2734 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 6 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 1 20 25 1 0 25 26 1 6 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 30 33 1 0 29 34 1 0 18 35 1 0 16 36 1 0 36 37 1 6 36 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 41 43 1 0 41 44 1 0 40 45 1 0 10 46 1 0 9 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 51 54 1 0 50 55 1 0 49 56 1 0 8 57 1 0 7 58 1 0 46 6 1 0 53 48 1 0 44 12 1 0 23 14 1 0 34 25 1 0 44 36 1 0 23 19 1 0 1 59 1 0 1 60 1 0 1 61 1 0 5 62 1 0 5 63 1 0 6 64 1 1 7 65 1 6 8 66 1 1 9 67 1 6 10 68 1 6 12 69 1 6 13 70 1 0 13 71 1 0 15 72 1 0 15 73 1 0 15 74 1 0 16 75 1 1 17 76 1 0 17 77 1 0 18 78 1 1 19 79 1 6 20 80 1 1 21 81 1 0 21 82 1 0 22 83 1 0 22 84 1 0 24 85 1 0 24 86 1 0 24 87 1 0 26 88 1 0 26 89 1 0 26 90 1 0 27 91 1 0 27 92 1 0 28 93 1 0 28 94 1 0 29 95 1 1 31 96 1 0 31 97 1 0 31 98 1 0 32 99 1 0 32100 1 0 32101 1 0 33102 1 0 35103 1 0 37104 1 0 37105 1 0 37106 1 0 38107 1 0 38108 1 0 39109 1 0 39110 1 0 40111 1 6 42112 1 0 42113 1 0 42114 1 0 43115 1 0 43116 1 0 43117 1 0 44118 1 1 45119 1 0 48120 1 6 49121 1 1 50122 1 6 51123 1 1 52124 1 0 52125 1 0 54126 1 0 55127 1 0 56128 1 0 57129 1 0 58130 1 0 M END

Standard InCHIKey	URPKGNJHPFKECW-MCQXXECASA-N
Standard InCHI	InChI=1S/C43H72O15/c1-20(44)53-19-25-31(49)32(50)34(57-36-33(51)30(48)23(46)18-54-36)37(56-25)55-24-17-42(8)26(40(6)13-11-27(47)38(2,3)35(24)40)16-22(45)29-21(10-14-41(29,42)7)43(9)15-12-28(58-43)39(4,5)52/h21-37,45-52H,10-19H2,1-9H3/t21-,22+,23+,24-,25+,26+,27-,28-,29-,30-,31+,32-,33+,34+,35-,36-,37+,40+,41+,42+,43-/m0/s1
SMILES	CC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](O[C@H]2C[C@]3(C)[C@H](C[C@H]([C@@H]4[C@H](CC[C@@]34C)[C@]3(C)CC[C@@H](C(C)(C)O)O3)O)[C@@]3(C)CC[C@@H](C(C)(C)[C@H]23)O)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	828.49	Volume:	821.606 ? Van der Waals volume.
Dense:	1.008	LogP:	1.894 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.594 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.709 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	38.0
TPSA:	234.29 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	8.0	Rings:	7.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.128	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.124	Fsp³:	0.977
MCE-18:	155.576 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.805	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.151	Promiscuous compounds:	0.414

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.912	MDCK Permeability:	-5.228
Pgp-inhibitor:	0.0	Pgp-substrate:	0.967
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.115	30% Bioavailability (F30%):	0.443
50% Bioavailability (F50%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.81	MRP1:	0.571
Plasma Protein Binding (PPB):	62.785%	Volume Distribution (VD):	-0.488
Fu:	29.6% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.03
BSEP inhibitor:	0.137

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.012	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.13
HLM stability:	0.181 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.833

Half-life (T1/2):

2.5

ADMET: Toxicity

hERG Blockers:	0.006	hERG Blockers (10um):	0.029
Human Hepatotoxicity (H-HT):	0.448	Drug-induced Liver Injury (DILI):	0.353
AMES Toxicity:	0.668	Rat Oral Acute Toxicity:	0.013
Maximum Recommended Daily Dose:	0.017	Skin Sensitization:	1.0
Carcinogencity:	0.282	Eye Corrosion:	0.0
Eye Irritation:	0.007	Respiratory Toxicity:	0.005
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.99
Hematotoxicity:	0.335	Drug-induced Nephrotoxicity:	0.965
Genotoxicity:	0.197	RPMI-8226 Immunitoxicity:	0.104
A549 Cytotoxicity:	0.19	Hek293 Cytotoxicity:	0.147
BCF:	0.455 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.274 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.931 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.946 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[11325227]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350149]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28006911]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28202328]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Inhibition	3
Activity	4
IC50	2
Survival	3

Activity Type	# Activity
Cell line	11
Organism	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	44.7	%	DOI[10.1007/s00044-012-0011-4]
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	143.8	%	DOI[10.1007/s00044-012-0011-4]
NPT993	Cell line	Hepatocyte	Mus musculus	Inhibition	=	72.9	%	DOI[10.1007/s00044-012-0011-4]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	19.0	%	PMID[25765759]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	61.3	%	DOI[10.1007/s00044-012-0011-4]
NPT993	Cell line	Hepatocyte	Mus musculus	Activity	=	31.1	%	DOI[10.1007/s00044-012-0011-4]
NPT993	Cell line	Hepatocyte	Mus musculus	IC50	=	63200.0	nM	PMID[15332862]
NPT136	Cell line	SK-N-SH	Homo sapiens	Activity	=	97.0	%	PubChem BioAssay data set

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	43.2	%	PMID[24893224]
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	72.9	%	PMID[24893224]
NPT993	Cell line	Hepatocyte	Mus musculus	Survival	=	51.7	%	DOI[10.1007/s00044-012-0011-4]
NPT32	Organism	Mus musculus	Mus musculus	IC50	=	63200.0	nM	PMID[29353722]

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC203434 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24087
0.1-0.2	22362
0.2-0.3	3055
0.3-0.4	272
0.4-0.5	61
0.5-0.6	8
0.6-0.7	5
0.7-0.8	0
0.8-0.85	1
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8681	High Similarity	NPC305418
0.8667	High Similarity	NPC237071
0.8667	High Similarity	NPC238796
0.8315	Intermediate Similarity	NPC210759
0.7174	Intermediate Similarity	NPC229801
0.6947	Remote Similarity	NPC307167
0.6571	Remote Similarity	NPC6931
0.6569	Remote Similarity	NPC160816
0.6484	Remote Similarity	NPC82955
0.6019	Remote Similarity	NPC286969
0.5728	Remote Similarity	NPC127801
0.5514	Remote Similarity	NPC208594
0.549	Remote Similarity	NPC473199
0.5429	Remote Similarity	NPC152584
0.5094	Remote Similarity	NPC472252
0.5094	Remote Similarity	NPC245280
0.5051	Remote Similarity	NPC131466
0.5049	Remote Similarity	NPC274833

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC203434 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7598
0.1-0.2	1513
0.2-0.3	39
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data