NPASS Compound

Natural Product: NPC2421

Natural Product ID	NPC2421
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WKKBYJLXSKPKSC-KWWNYLJESA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
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 105110 0 0 0 0 0 0 0 0999 V2000 2.8855 -2.4464 -4.3481 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7894 -2.6473 -2.8540 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8693 -1.8270 -2.2016 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6204 -1.8911 -0.7163 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3866 -1.0223 -0.4015 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8769 -1.3254 0.9493 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4490 -1.2267 1.2518 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5032 -0.9239 0.1566 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3374 -2.1790 -0.0683 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1258 -0.5375 -1.1426 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5004 0.3092 -1.9733 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8107 0.9422 -1.7464 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4415 0.3470 -0.5608 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7559 1.0106 -0.1571 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5589 2.3585 0.4608 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5215 1.2233 -1.4505 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9923 1.3700 -1.2678 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5441 0.3199 -0.3735 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8626 0.2281 0.9816 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2689 1.3076 1.8953 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3974 -1.0856 1.5702 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8046 -0.9867 1.6693 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4089 0.0180 0.7434 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5990 -0.1541 1.9788 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1435 -0.1989 1.8691 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4971 0.1934 0.5717 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6010 1.4030 0.7436 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4766 -0.9054 -1.0487 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3955 2.6644 -0.9476 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4531 -1.0654 -1.5473 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4077 -2.3640 -2.3055 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5195 -2.1746 -3.5225 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9907 -3.4530 -1.6159 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9766 0.3699 -0.3476 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5768 1.2613 -1.1402 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9642 0.6803 0.5752 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5068 1.9638 0.6235 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2508 2.6561 1.9439 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9585 1.9802 3.0711 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9152 0.9525 2.5446 C 0 0 1 0 0 0 0 0 0 0 0 0 6.6464 1.3981 1.3207 C 0 0 1 0 0 0 0 0 0 0 0 0 7.4491 0.1944 0.8144 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2580 -0.3231 1.7975 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8500 1.8909 0.3184 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8749 0.7353 3.5574 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0004 1.3639 3.8935 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6875 3.9638 1.8293 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8776 -1.3856 -4.6499 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8991 -2.8352 -4.6525 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1654 -3.0790 -4.9029 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0786 -3.7269 -2.6806 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9115 -0.7876 -2.5220 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8462 -2.3516 -2.3850 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5032 -2.9087 -0.3370 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5306 -1.4637 -0.2235 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4892 -0.7545 1.7175 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2085 -2.3903 1.1710 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3030 -0.4369 2.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1112 -2.1437 1.8387 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2989 -2.1452 0.4866 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8288 -3.0830 0.3863 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5997 -2.3459 -1.1287 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0039 0.5604 -2.9141 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7862 2.0526 -1.7851 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4330 0.6600 -2.6616 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7587 -0.6994 -0.8626 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1938 2.3449 1.4948 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5827 2.8319 0.5120 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9939 3.0020 -0.2293 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1372 2.1440 -1.9354 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3579 0.3144 -2.0899 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4527 1.1759 -2.2849 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6397 0.5147 -0.2302 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5110 1.8179 2.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0664 0.9970 2.6356 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7887 2.1042 1.2847 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9548 -1.3113 2.5531 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2023 -1.8602 0.8011 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2532 -1.2081 0.8246 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3545 -0.9774 0.1997 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9314 0.5811 2.7733 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9407 -1.1393 2.4283 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6994 0.4869 2.6554 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7190 -1.1981 2.1940 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7611 2.1634 -0.0712 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4714 1.1426 0.8356 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8322 1.9706 1.6681 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9180 -0.7518 -1.9275 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5250 3.2412 -1.7250 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8959 -0.3654 -2.3338 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8880 -1.4113 -4.2139 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4719 -1.8337 -3.1648 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3394 -3.1592 -4.0044 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7249 -4.1018 -1.4203 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0222 2.5878 -0.1532 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1454 2.6736 2.0760 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5478 2.7271 3.6624 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4149 -0.0208 2.3884 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3831 2.1758 1.6004 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0318 0.5360 -0.0631 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7030 -0.5690 0.5181 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1878 -0.1888 1.5431 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1597 1.5982 3.9525 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0994 1.4023 3.5153 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1819 4.4586 1.1234 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 7 8 1 0 8 9 1 6 8 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 1 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 1 19 21 1 0 21 22 1 0 19 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 1 18 28 1 0 17 29 1 0 10 30 1 0 30 31 1 0 31 32 1 0 31 33 1 1 5 34 1 1 34 35 2 0 34 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 41 44 1 0 40 45 1 0 39 46 1 0 38 47 1 0 31 2 1 0 44 37 1 0 30 5 1 0 26 8 1 0 26 13 1 0 23 14 1 0 1 48 1 0 1 49 1 0 1 50 1 0 2 51 1 6 3 52 1 0 3 53 1 0 4 54 1 0 4 55 1 0 6 56 1 0 6 57 1 0 7 58 1 0 7 59 1 0 9 60 1 0 9 61 1 0 9 62 1 0 11 63 1 0 12 64 1 0 12 65 1 0 13 66 1 6 15 67 1 0 15 68 1 0 15 69 1 0 16 70 1 0 16 71 1 0 17 72 1 6 18 73 1 1 20 74 1 0 20 75 1 0 20 76 1 0 21 77 1 0 21 78 1 0 22 79 1 0 23 80 1 6 24 81 1 0 24 82 1 0 25 83 1 0 25 84 1 0 27 85 1 0 27 86 1 0 27 87 1 0 28 88 1 0 29 89 1 0 30 90 1 6 32 91 1 0 32 92 1 0 32 93 1 0 33 94 1 0 37 95 1 6 38 96 1 1 39 97 1 1 40 98 1 6 41 99 1 1 42100 1 0 42101 1 0 43102 1 0 45103 1 0 46104 1 0 47105 1 0 M END

Standard InCHIKey	WKKBYJLXSKPKSC-KWWNYLJESA-N
Standard InCHI	InChI=1S/C36H58O11/c1-18-9-12-36(30(44)47-29-26(42)25(41)24(40)21(16-37)46-29)14-13-33(4)19(27(36)35(18,6)45)7-8-23-31(2)15-20(39)28(43)32(3,17-38)22(31)10-11-34(23,33)5/h7,18,20-29,37-43,45H,8-17H2,1-6H3/t18-,20-,21+,22+,23+,24+,25-,26+,27+,28+,29-,31-,32-,33+,34+,35+,36-/m0/s1
SMILES	C[C@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C[C@@H]([C@H]([C@@](C)(CO)[C@@H]5CC[C@@]34C)O)O)[C@@H]2[C@]1(C)O)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	666.4	Volume:	671.293 ? Van der Waals volume.
Dense:	0.993	LogP:	1.216 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.808 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.4 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	33.0
TPSA:	197.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	8.0	Rings:	6.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.16	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.655	Fsp³:	0.917
MCE-18:	133.507 ? 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:	0.713	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.033 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.163	Promiscuous compounds:	0.187

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.252	MDCK Permeability:	-5.138
Pgp-inhibitor:	0.0	Pgp-substrate:	0.404
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):	0.04
20% Bioavailability (F20%):	0.766	30% Bioavailability (F30%):	0.965
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.134	MRP1:	0.41
Plasma Protein Binding (PPB):	71.978%	Volume Distribution (VD):	-0.242
Fu:	21.739% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.015
BSEP inhibitor:	0.042

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:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.011
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):

1.368

Half-life (T1/2):

2.865

ADMET: Toxicity

hERG Blockers:	0.005	hERG Blockers (10um):	0.026
Human Hepatotoxicity (H-HT):	0.592	Drug-induced Liver Injury (DILI):	0.236
AMES Toxicity:	0.789	Rat Oral Acute Toxicity:	0.02
Maximum Recommended Daily Dose:	0.033	Skin Sensitization:	0.999
Carcinogencity:	0.562	Eye Corrosion:	0.0
Eye Irritation:	0.008	Respiratory Toxicity:	0.04
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.99
Hematotoxicity:	0.393	Drug-induced Nephrotoxicity:	0.951
Genotoxicity:	0.49	RPMI-8226 Immunitoxicity:	0.084
A549 Cytotoxicity:	0.653	Hek293 Cytotoxicity:	0.279
BCF:	1.029 ? 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:	3.483 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.994 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.16 ? 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
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/0031-9422(86)88033-5]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/0031-9422(86)88033-5]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	whole plant	n.a.	n.a.	DOI[10.1016/j.tetlet.2016.12.029]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	whole plant	n.a.	DOI[10.1021/np50028a032]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[10993241]
NPO17628	Rabdosia excisa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043413]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	roots	n.a.	n.a.	PMID[15620235]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	roots	Nanning City, Guangxi Province, People's Republic of China	1997-Jan	PMID[17190442]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38732062]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[8759159]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8759159]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834152]
NPO11222	Rubus alceifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17628	Rabdosia excisa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26876	Rubus parviforlius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17628	Rabdosia excisa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26876	Rubus parviforlius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11222	Rubus alceifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17628	Rabdosia excisa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11222	Rubus alceifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3129	Geum japonicum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17628	Rabdosia excisa	Species	Lamiaceae	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

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

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 NPC2421 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	19278
0.1-0.2	25268
0.2-0.3	4117
0.3-0.4	950
0.4-0.5	156
0.5-0.6	48
0.6-0.7	19
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC271138
0.8831	High Similarity	NPC310014
0.8831	High Similarity	NPC269315
0.8228	Intermediate Similarity	NPC37739
0.7875	Intermediate Similarity	NPC116794
0.7805	Intermediate Similarity	NPC102914
0.7805	Intermediate Similarity	NPC110139
0.7805	Intermediate Similarity	NPC108709
0.775	Intermediate Similarity	NPC46388
0.7683	Intermediate Similarity	NPC68419
0.75	Intermediate Similarity	NPC220984
0.7159	Intermediate Similarity	NPC189884
0.7159	Intermediate Similarity	NPC138334
0.7045	Intermediate Similarity	NPC47063
0.6966	Remote Similarity	NPC204458
0.6905	Remote Similarity	NPC605954
0.686	Remote Similarity	NPC7870
0.686	Remote Similarity	NPC75747
0.6596	Remote Similarity	NPC58448
0.6552	Remote Similarity	NPC199457
0.6477	Remote Similarity	NPC212968
0.6437	Remote Similarity	NPC237503
0.6392	Remote Similarity	NPC75417
0.6364	Remote Similarity	NPC68175
0.6329	Remote Similarity	NPC259788
0.6329	Remote Similarity	NPC255589
0.6327	Remote Similarity	NPC160415
0.6292	Remote Similarity	NPC187056
0.6292	Remote Similarity	NPC604133
0.6292	Remote Similarity	NPC606216
0.6292	Remote Similarity	NPC607023
0.6111	Remote Similarity	NPC137917
0.6023	Remote Similarity	NPC167383
0.5977	Remote Similarity	NPC191763
0.5955	Remote Similarity	NPC285576
0.5922	Remote Similarity	NPC134835
0.5865	Remote Similarity	NPC73318
0.5849	Remote Similarity	NPC36831
0.5833	Remote Similarity	NPC29069
0.5773	Remote Similarity	NPC179434
0.5652	Remote Similarity	NPC65590
0.5652	Remote Similarity	NPC125923
0.5652	Remote Similarity	NPC306746
0.56	Remote Similarity	NPC150400
0.5579	Remote Similarity	NPC256798
0.55	Remote Similarity	NPC139894
0.549	Remote Similarity	NPC473343
0.5426	Remote Similarity	NPC64106
0.5417	Remote Similarity	NPC128925
0.5408	Remote Similarity	NPC90856
0.5408	Remote Similarity	NPC214484
0.5361	Remote Similarity	NPC209894
0.5347	Remote Similarity	NPC235405
0.5321	Remote Similarity	NPC481030
0.53	Remote Similarity	NPC48499
0.5294	Remote Similarity	NPC473373
0.5294	Remote Similarity	NPC249848
0.5294	Remote Similarity	NPC107966
0.5253	Remote Similarity	NPC269095
0.5243	Remote Similarity	NPC295371
0.5243	Remote Similarity	NPC473884
0.5243	Remote Similarity	NPC39211
0.5217	Remote Similarity	NPC240125
0.5213	Remote Similarity	NPC190837
0.52	Remote Similarity	NPC78046
0.5196	Remote Similarity	NPC475516
0.5192	Remote Similarity	NPC475171
0.5192	Remote Similarity	NPC469946
0.5182	Remote Similarity	NPC96641
0.5182	Remote Similarity	NPC163183
0.514	Remote Similarity	NPC235438
0.5104	Remote Similarity	NPC48249
0.5096	Remote Similarity	NPC157868
0.5094	Remote Similarity	NPC109588
0.5094	Remote Similarity	NPC30735
0.5093	Remote Similarity	NPC222580
0.5048	Remote Similarity	NPC161674
0.5047	Remote Similarity	NPC40775
0.5047	Remote Similarity	NPC10607
0.5047	Remote Similarity	NPC46665
0.5046	Remote Similarity	NPC601659

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC2421 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7152
0.1-0.2	1935
0.2-0.3	60
0.3-0.4	3
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