NPASS Compound

Natural Product: NPC238935

Natural Product ID	NPC238935
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-O-Beta-D-Glucopyranosyl-28-O-Alpha-L-Rhamnopyranosyl-16Alpha-Hydrox Y-23-Deoxyprotobassic Acid
IUPAC Name	[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl] (4aR,5R,6aR,6aS,6bR,8R,8aR,10R,11S,12aR,14bS)-5,8,11-trihydroxy-2,2,6a,6b,9,9,12a-heptamethyl-10-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL503292
PubChem CID	21672204
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 125131 0 0 0 0 0 0 0 0999 V2000 -9.8447 -0.6905 0.2411 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4773 -1.1471 -0.2346 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.2606 -2.5647 0.2382 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1865 -3.2822 -0.5100 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1043 -2.8949 -1.9756 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1614 -1.3848 -2.0378 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.4510 -1.0331 -1.6087 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2049 -0.8937 -1.1164 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1902 -0.0280 -1.4327 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0717 0.3761 -2.6051 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2002 0.4569 -0.3885 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1460 1.1033 0.6397 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4823 2.1086 1.5057 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9441 3.2101 0.6606 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7620 3.8479 1.3556 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0460 4.2897 0.6289 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7040 2.8256 -0.7443 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2827 1.4099 -1.0167 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8379 1.1420 -0.8648 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9829 1.9112 -1.4847 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4971 1.8176 -1.4703 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9667 0.6326 -0.7054 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4139 0.2639 -0.9279 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8451 0.2938 -2.3501 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2439 1.3359 -0.2062 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9511 0.8000 0.9991 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8802 -0.3597 0.6167 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0777 -1.4427 -0.0321 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7384 -2.0301 -1.2349 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0167 -2.5854 1.0082 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6551 -1.0239 -0.2167 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7588 -2.1503 -0.6685 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3555 -1.7793 -0.2433 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0168 -0.4692 -0.8268 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4964 -0.7021 -2.2447 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2639 0.0277 -0.0593 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8957 0.5477 1.2852 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2240 -1.1071 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6311 -0.7365 0.2827 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7604 -0.6768 1.6815 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7650 -2.4218 -1.9975 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8562 0.2093 -0.1853 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1086 0.2215 0.4000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.1423 -0.5340 -0.3689 C 0 0 1 0 0 0 0 0 0 0 0 0 9.5018 -0.1640 0.1077 C 0 0 2 0 0 0 0 0 0 0 0 0 9.5727 0.5053 1.4395 C 0 0 1 0 0 0 0 0 0 0 0 0 8.4241 1.4147 1.7259 C 0 0 1 0 0 0 0 0 0 0 0 0 8.8661 2.7353 2.2550 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6685 2.4754 3.3782 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5966 1.5230 0.5813 O 0 0 0 0 0 0 0 0 0 0 0 0 9.6197 -0.4837 2.4194 O 0 0 0 0 0 0 0 0 0 0 0 0 10.1503 0.6750 -0.8151 O 0 0 0 0 0 0 0 0 0 0 0 0 7.9678 -1.9173 -0.2864 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8337 1.8278 1.4143 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1327 -3.4863 -2.7098 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3479 -4.6625 -0.3917 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8491 -2.4651 1.5866 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.8577 0.3884 0.4676 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6172 -0.8474 -0.5640 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1760 -1.3166 1.1004 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7137 -0.4437 0.1726 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2069 -3.1174 0.2089 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2092 -3.0111 -0.0432 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0928 -3.2181 -2.3488 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9796 -0.9871 -3.0686 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5634 0.3046 1.2865 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0146 1.5796 0.1470 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6837 1.7425 2.1517 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2736 2.4907 2.2011 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0148 4.2561 0.6766 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3310 3.1488 2.1322 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1452 4.6951 1.9600 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1176 4.7891 1.6166 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8792 4.9763 -0.2066 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0359 3.7598 0.5055 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6934 2.9408 -1.2922 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0563 3.5682 -1.2655 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4321 1.3411 -2.1578 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3717 2.7441 -2.1033 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9147 2.7761 -1.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7928 1.8121 -2.5414 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9434 0.9712 0.3777 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9670 0.1510 -2.3994 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4262 -0.4362 -3.0227 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7487 1.3605 -2.7120 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0101 1.7896 -0.8661 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6112 2.1839 0.1352 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3281 0.5863 1.8651 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3765 -0.6689 1.5591 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1017 -2.2160 -2.0945 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2317 -3.0270 -1.0210 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6035 -1.4014 -1.5994 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1059 -3.5688 0.5183 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8681 -2.5123 1.7194 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1057 -2.5458 1.6018 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2909 -0.8306 0.8467 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0740 -3.0470 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3336 -1.8179 0.8595 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3659 -2.5416 -0.6191 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0611 -0.1021 -2.9903 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5609 -0.4384 -2.4032 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4036 -1.7666 -2.5684 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0684 -0.0184 1.7723 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7012 1.6357 1.3030 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7444 0.4089 2.0202 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2017 -1.6991 -0.9504 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8810 -1.7945 0.7909 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2436 -1.6482 0.0034 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3620 -1.3310 2.0636 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7229 -3.3832 -2.2334 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9956 -0.2581 1.3943 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0466 -0.1981 -1.4440 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1391 -1.0953 0.1327 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5121 1.0990 1.5692 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7499 0.9249 2.4810 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9546 3.2532 2.6680 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3978 3.3629 1.5430 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3677 1.6995 3.8858 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4085 -1.0790 2.2078 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2974 1.5767 -0.4870 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1402 -2.2813 -1.1905 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3173 2.6508 1.6328 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3248 -4.3524 -2.2681 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6273 -4.8425 0.5494 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5090 -1.9955 2.1275 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 2 0 11 9 1 6 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 16 1 0 14 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 28 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 6 34 36 1 0 36 37 1 1 36 38 1 0 38 39 1 0 39 40 1 0 32 41 1 0 27 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 47 50 1 0 46 51 1 0 45 52 1 0 44 53 1 0 26 54 1 0 5 55 1 0 4 56 1 0 3 57 1 0 7 2 1 0 18 11 1 0 36 19 1 0 50 43 1 0 39 11 1 0 34 22 1 0 31 23 1 0 1 58 1 0 1 59 1 0 1 60 1 0 2 61 1 1 3 62 1 1 4 63 1 1 5 64 1 6 6 65 1 6 12 66 1 0 12 67 1 0 13 68 1 0 13 69 1 0 15 70 1 0 15 71 1 0 15 72 1 0 16 73 1 0 16 74 1 0 16 75 1 0 17 76 1 0 17 77 1 0 18 78 1 6 20 79 1 0 21 80 1 0 21 81 1 0 22 82 1 1 24 83 1 0 24 84 1 0 24 85 1 0 25 86 1 0 25 87 1 0 26 88 1 1 27 89 1 1 29 90 1 0 29 91 1 0 29 92 1 0 30 93 1 0 30 94 1 0 30 95 1 0 31 96 1 1 32 97 1 1 33 98 1 0 33 99 1 0 35100 1 0 35101 1 0 35102 1 0 37103 1 0 37104 1 0 37105 1 0 38106 1 0 38107 1 0 39108 1 6 40109 1 0 41110 1 0 43111 1 1 44112 1 6 45113 1 1 46114 1 6 47115 1 1 48116 1 0 48117 1 0 49118 1 0 51119 1 0 52120 1 0 53121 1 0 54122 1 0 55123 1 0 56124 1 0 57125 1 0 M END

Standard InCHIKey	LZIMOIPXNDCZGQ-RFFVNIRISA-N
Standard InCHI	InChI=1S/C42H68O15/c1-18-26(47)28(49)30(51)34(54-18)57-36(53)42-12-11-37(2,3)13-20(42)19-9-10-24-39(6)14-22(45)33(56-35-31(52)29(50)27(48)23(17-43)55-35)38(4,5)32(39)21(44)15-41(24,8)40(19,7)16-25(42)46/h9,18,20-35,43-52H,10-17H2,1-8H3/t18-,20-,21+,22-,23+,24+,25+,26-,27+,28+,29-,30+,31+,32-,33-,34-,35-,39+,40+,41+,42+/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H](C(C)(C)[C@@H]4[C@@H](C[C@@]3(C)[C@]1(C)C[C@H]2O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	812.46	Volume:	801.673 ? Van der Waals volume.
Dense:	1.013	LogP:	1.709 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.287 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.732 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	39.0
TPSA:	256.29 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	10.0	Rings:	7.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.102	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.133	Fsp³:	0.929
MCE-18:	158.963 ? 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:	0.707	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.028 ? 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:	0.177	Promiscuous compounds:	0.114

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.064	MDCK Permeability:	-5.21
Pgp-inhibitor:	0.0	Pgp-substrate:	0.837
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):	0.762
20% Bioavailability (F20%):	0.778	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.056	MRP1:	0.161
Plasma Protein Binding (PPB):	78.345%	Volume Distribution (VD):	-0.301
Fu:	12.538% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.0

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:	0.001
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	0.004
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.004
HLM stability:	0.005 ? 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):

0.689

Half-life (T1/2):

3.872

ADMET: Toxicity

hERG Blockers:	0.004	hERG Blockers (10um):	0.011
Human Hepatotoxicity (H-HT):	0.686	Drug-induced Liver Injury (DILI):	0.736
AMES Toxicity:	0.908	Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.006	Skin Sensitization:	1.0
Carcinogencity:	0.12	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.006
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.998
Hematotoxicity:	0.746	Drug-induced Nephrotoxicity:	0.968
Genotoxicity:	0.287	RPMI-8226 Immunitoxicity:	0.205
A549 Cytotoxicity:	0.933	Hek293 Cytotoxicity:	0.327
BCF:	1.007 ? 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:	3.338 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.739 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.873 ? 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
NPO15083	Mussaenda macrophylla	Species	Rubiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[10543897]
NPO15083	Mussaenda macrophylla	Species	Rubiaceae	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
MIC	2

Activity Type	# Activity
Organism	2

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
NPT878	Organism	Streptococcus mutans	Streptococcus mutans	MIC	>	1250.0	ug.mL-1	PMID[23368966]
NPT1127	Organism	Porphyromonas gingivalis	Porphyromonas gingivalis	MIC	=	312.0	ug.mL-1	PMID[21524573]

In vivo activity

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

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 NPC238935 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	21254
0.1-0.2	23745
0.2-0.3	3723
0.3-0.4	813
0.4-0.5	269
0.5-0.6	43
0.6-0.7	6
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	Natural Product ID
0.7955	Intermediate Similarity	NPC475208
0.7442	Intermediate Similarity	NPC48249
0.66	Remote Similarity	NPC164389
0.6526	Remote Similarity	NPC1046
0.6486	Remote Similarity	NPC237191
0.6263	Remote Similarity	NPC480420
0.6095	Remote Similarity	NPC64715
0.6022	Remote Similarity	NPC306746
0.5962	Remote Similarity	NPC305267
0.5913	Remote Similarity	NPC21691
0.5851	Remote Similarity	NPC199457
0.5818	Remote Similarity	NPC815
0.5804	Remote Similarity	NPC123522
0.5678	Remote Similarity	NPC475514
0.5636	Remote Similarity	NPC69811
0.5593	Remote Similarity	NPC286457
0.5586	Remote Similarity	NPC104137
0.5586	Remote Similarity	NPC26626
0.5574	Remote Similarity	NPC220160
0.5546	Remote Similarity	NPC470876
0.5537	Remote Similarity	NPC302543
0.5536	Remote Similarity	NPC11242
0.5517	Remote Similarity	NPC283417
0.5517	Remote Similarity	NPC200049
0.5481	Remote Similarity	NPC150400
0.5472	Remote Similarity	NPC112352
0.5462	Remote Similarity	NPC473452
0.5446	Remote Similarity	NPC214484
0.5424	Remote Similarity	NPC4749
0.5368	Remote Similarity	NPC167383
0.5351	Remote Similarity	NPC213952
0.5258	Remote Similarity	NPC237503
0.5234	Remote Similarity	NPC76497
0.5229	Remote Similarity	NPC46665
0.521	Remote Similarity	NPC25663
0.5167	Remote Similarity	NPC85154
0.5161	Remote Similarity	NPC144644
0.5161	Remote Similarity	NPC37860
0.5161	Remote Similarity	NPC170407
0.514	Remote Similarity	NPC39211
0.5126	Remote Similarity	NPC480423
0.5098	Remote Similarity	NPC209894
0.5094	Remote Similarity	NPC475516
0.5085	Remote Similarity	NPC475899
0.5079	Remote Similarity	NPC142151
0.5079	Remote Similarity	NPC267694
0.5077	Remote Similarity	NPC480421
0.5048	Remote Similarity	NPC48499
0.5046	Remote Similarity	NPC223301
0.5046	Remote Similarity	NPC171544
0.5044	Remote Similarity	NPC114484

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC238935 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7382
0.1-0.2	1700
0.2-0.3	62
0.3-0.4	6
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