NPASS Compound

Natural Product: NPC113500

Natural Product ID	NPC113500
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Certonardoside F
IUPAC Name	(3S,4R,5S,6S,8S,9R,10S,13R,14S,15R,17R)-17-[(2R,5S)-5-[(2R,3R,4S,5R)-4-hydroxy-3-[(2S,3R,4S,5R)-4-hydroxy-3,5-dimethoxyoxan-2-yl]oxy-5-(hydroxymethyl)oxolan-2-yl]oxy-6-methylheptan-2-yl]-10,13-dimethyl-1,2,3,4,5,6,7,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthrene-3,4,6,8,15-pentol
Synonyms	Certonardoside F
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL500265
PubChem CID	44567122
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

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 121126 0 0 0 0 0 0 0 0999 V2000 2.0171 0.0228 1.9385 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4396 0.6287 0.6269 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8065 1.2425 0.8062 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4768 -0.3124 -0.5086 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1233 -0.9701 -0.8285 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0712 0.0450 -1.1970 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2550 -0.4611 -1.5459 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1582 -1.4205 -2.7458 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2493 -0.9372 -0.6458 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0807 -2.0684 0.2787 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3969 -2.0685 1.0919 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1052 -0.8867 0.6128 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9635 0.0667 0.2496 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1472 0.4636 1.4298 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5651 1.1940 -0.5163 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6611 1.8398 0.3282 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7535 0.8139 0.4764 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0836 1.3422 0.8195 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.1069 2.3429 1.9457 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5885 2.0888 -0.4232 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0197 2.4630 -0.3570 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9393 1.3471 0.0673 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4450 0.6344 1.3028 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.0323 0.2182 1.0636 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.5048 -0.7211 2.1471 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.2686 -1.3522 1.5421 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2033 -0.2823 1.3773 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8909 0.1608 2.6380 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4874 -1.6880 2.3449 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.6083 1.3808 2.4499 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1749 1.9127 0.3798 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1826 -2.1586 2.4403 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5005 -1.2269 -0.5429 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3455 -1.1736 -1.5893 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7667 -1.1031 -1.1233 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1352 -2.5645 -0.9804 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1271 -3.2449 -1.8353 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2262 -4.1810 -1.0579 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9547 -5.1904 -0.4311 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3308 -2.2924 -2.4165 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1434 -2.9773 0.3444 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5949 -0.4472 -2.0269 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1751 0.6355 -1.3939 C 0 0 1 0 0 0 0 0 0 0 0 0 8.6879 0.5699 -1.3692 C 0 0 1 0 0 0 0 0 0 0 0 0 9.1161 1.4862 -0.2187 C 0 0 2 0 0 0 0 0 0 0 0 0 8.3121 2.7559 -0.3778 C 0 0 1 0 0 0 0 0 0 0 0 0 7.6464 2.8544 -1.7206 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7900 1.8260 -2.0180 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4019 2.9367 0.6409 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6957 4.0840 1.3798 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4665 1.7077 -0.3308 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1063 -0.7220 -1.1714 O 0 0 0 0 0 0 0 0 0 0 0 0 9.8883 -1.1127 -2.2406 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8846 -0.4877 2.4519 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7436 0.8653 2.6076 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1415 -0.6333 1.8721 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7236 1.4537 0.4194 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4101 0.5800 1.4576 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7614 2.2236 1.3213 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3116 1.2986 -0.1730 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6261 0.3233 -1.4388 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7659 -1.5262 0.0567 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3466 -1.6637 -1.6652 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4846 0.5453 -2.1326 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0319 0.8911 -0.4769 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7573 0.4489 -2.0770 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5983 -0.9726 -3.5667 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8511 -2.4230 -2.4536 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2231 -1.5082 -3.1093 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1094 -1.2867 -1.3330 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2925 -1.9963 1.0455 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9443 -3.0276 -0.2442 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9563 -2.9865 0.7692 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5374 -1.1518 -0.4043 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5732 0.1734 2.4138 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0778 1.5882 1.4705 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1213 0.0100 1.4291 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0585 0.7802 -1.4079 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8171 1.9671 -0.7611 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2638 2.1874 1.3017 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9777 2.7426 -0.2202 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8443 0.3260 -0.5414 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9832 3.0402 1.7884 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2250 2.9946 1.9508 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3204 1.8693 2.9341 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4504 1.4163 -1.3187 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9929 2.9874 -0.6353 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3305 2.7227 -1.4131 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2450 3.3799 0.2257 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1120 0.6216 -0.7508 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0570 -0.2871 1.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0338 -0.4154 0.1283 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2888 -0.1643 3.0812 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8492 -2.1556 2.2033 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5850 -1.7816 0.5634 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0537 1.0939 2.8271 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6831 -2.1052 1.4668 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7226 0.7534 3.2073 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.0626 2.4024 1.2352 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9934 -3.0976 2.7155 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1150 -0.3154 -2.2896 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7779 -0.5929 -0.1296 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1780 -2.6677 -1.3714 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6682 -3.8738 -2.5849 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5282 -4.6755 -1.7627 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6901 -3.6312 -0.2502 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4080 -5.6940 0.2176 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9128 -3.5758 0.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8265 0.6700 -0.3497 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0505 1.0156 -2.3106 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8863 1.0053 0.7536 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0539 3.5985 -0.3346 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0796 3.8157 -1.7252 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4451 2.9933 -2.4969 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6837 5.0042 0.7931 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0059 4.2037 2.2345 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7137 3.9087 1.8207 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9790 0.8674 -0.4124 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7839 -0.4903 -2.3804 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1799 -2.1746 -2.1071 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3206 -1.0605 -3.2042 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 1 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 1 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 1 25 29 1 0 23 30 1 0 22 31 1 0 11 32 1 0 4 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 37 40 1 0 36 41 1 0 35 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 46 49 1 0 49 50 1 0 45 51 1 0 44 52 1 0 52 53 1 0 13 9 1 0 27 17 1 0 40 34 1 0 48 43 1 0 27 12 1 0 24 18 1 0 1 54 1 0 1 55 1 0 1 56 1 0 2 57 1 0 3 58 1 0 3 59 1 0 3 60 1 0 4 61 1 6 5 62 1 0 5 63 1 0 6 64 1 0 6 65 1 0 7 66 1 6 8 67 1 0 8 68 1 0 8 69 1 0 9 70 1 6 10 71 1 0 10 72 1 0 11 73 1 6 12 74 1 6 14 75 1 0 14 76 1 0 14 77 1 0 15 78 1 0 15 79 1 0 16 80 1 0 16 81 1 0 17 82 1 6 19 83 1 0 19 84 1 0 19 85 1 0 20 86 1 0 20 87 1 0 21 88 1 0 21 89 1 0 22 90 1 6 23 91 1 1 24 92 1 6 25 93 1 1 26 94 1 0 26 95 1 0 28 96 1 0 29 97 1 0 30 98 1 0 31 99 1 0 32100 1 0 34101 1 6 35102 1 1 36103 1 6 37104 1 6 38105 1 0 38106 1 0 39107 1 0 41108 1 0 43109 1 1 44110 1 6 45111 1 1 46112 1 6 47113 1 0 47114 1 0 50115 1 0 50116 1 0 50117 1 0 51118 1 0 53119 1 0 53120 1 0 53121 1 0 M END

Standard InCHIKey	WRQWUNHMUXGXID-HPWQZGQYSA-N
Standard InCHI	InChI=1S/C39H68O14/c1-18(2)24(51-36-33(30(45)25(16-40)52-36)53-35-32(49-7)31(46)26(48-6)17-50-35)9-8-19(3)20-14-22(42)34-37(20,4)13-11-27-38(5)12-10-21(41)29(44)28(38)23(43)15-39(27,34)47/h18-36,40-47H,8-17H2,1-7H3/t19-,20-,21+,22-,23+,24+,25-,26-,27-,28+,29+,30+,31+,32-,33-,34-,35+,36-,37-,38-,39+/m1/s1
SMILES	CC(C)[C@H](CC[C@@H](C)[C@H]1C[C@H]([C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@@H]([C@@H]([C@@H]3[C@H](C[C@@]21O)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO)O1)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)OC)O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	760.46	Volume:	754.824 ? Van der Waals volume.
Dense:	1.007	LogP:	1.111 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.723 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.737 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	12.0	Rigid Bonds:	31.0
TPSA:	217.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	8.0	Rings:	6.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.138	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.056	Fsp³:	1.0
MCE-18:	122.667 ? 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:	0.612	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? 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:	0.305	Promiscuous compounds:	0.308

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.882	MDCK Permeability:	-5.278
Pgp-inhibitor:	0.0	Pgp-substrate:	0.991
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):	0.565
20% Bioavailability (F20%):	0.974	30% Bioavailability (F30%):	0.995
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.766
Plasma Protein Binding (PPB):	71.886%	Volume Distribution (VD):	-0.21
Fu:	27.423% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.963	BCRP inhibitor:	0.001
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:	0.138	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.009 ? 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):

2.039

Half-life (T1/2):

2.606

ADMET: Toxicity

hERG Blockers:	0.009	hERG Blockers (10um):	0.015
Human Hepatotoxicity (H-HT):	0.628	Drug-induced Liver Injury (DILI):	0.466
AMES Toxicity:	0.871	Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.006	Skin Sensitization:	1.0
Carcinogencity:	0.467	Eye Corrosion:	0.0
Eye Irritation:	0.051	Respiratory Toxicity:	0.011
Drug-induced Neurotoxicity:	0.006	Ototoxicity:	0.994
Hematotoxicity:	0.78	Drug-induced Nephrotoxicity:	0.99
Genotoxicity:	0.034	RPMI-8226 Immunitoxicity:	0.245
A549 Cytotoxicity:	0.606	Hek293 Cytotoxicity:	0.31
BCF:	1.152 ? 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:	3.358 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.714 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.81 ? 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
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444692]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662097]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104487]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497935]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
EC50	7
CC50	3

Activity Type	# Activity
Cell line	3
Organism	7

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
NPT165	Cell line	HeLa	Homo sapiens	CC50	=	64.8	ug.mL-1	PMID[23387824]
NPT25	Cell line	MT4	Homo sapiens	CC50	=	39.7	ug.mL-1	PubChem BioAssay data set
NPT189	Cell line	Vero	Chlorocebus aethiops	CC50	>	100.0	ug.mL-1	DrugMatrix in vitro pharmacology data
NPT190	Organism	Human herpesvirus 1	Human herpesvirus 1	EC50	>	100.0	ug.mL-1	PMID[9392889]
NPT1141	Organism	Human herpesvirus 2	Human herpesvirus 2	EC50	>	100.0	ug.mL-1	PMID[22360639]
NPT3119	Organism	Human coxsackievirus B3	Human coxsackievirus B3	EC50	>	64.8	ug.mL-1	PMID[23252603]
NPT4337	Organism	Encephalomyocarditis virus	Encephalomyocarditis virus	EC50	>	64.8	ug.mL-1	PMID[24099080]
NPT3795	Organism	Human immunodeficiency virus 2	Human immunodeficiency virus 2	EC50	>	39.7	ug.mL-1	PMID[25894905]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	>	39.7	ug.mL-1	PMID[20100877]
NPT2516	Organism	Vesicular stomatitis Indiana virus	Vesicular stomatitis Indiana virus	EC50	>	64.8	ug.mL-1	PMID[21741249]

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 NPC113500 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	23491
0.1-0.2	24688
0.2-0.3	1619
0.3-0.4	26
0.4-0.5	19
0.5-0.6	9
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC3538
0.7927	Intermediate Similarity	NPC311246
0.7927	Intermediate Similarity	NPC167644
0.7416	Intermediate Similarity	NPC473638
0.7143	Intermediate Similarity	NPC149966
0.6556	Remote Similarity	NPC477224
0.5824	Remote Similarity	NPC5632
0.5699	Remote Similarity	NPC475521
0.519	Remote Similarity	NPC192046
0.5128	Remote Similarity	NPC105208
0.5128	Remote Similarity	NPC302578
0.5128	Remote Similarity	NPC477227
0.5122	Remote Similarity	NPC121981
0.5102	Remote Similarity	NPC483923
0.5062	Remote Similarity	NPC128951

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC113500 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7416
0.1-0.2	1708
0.2-0.3	26
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