NPASS Compound

Natural Product: NPC471089

Natural Product ID	NPC471089
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Yadanzioside G
IUPAC Name	n.a.
Synonyms	Yadanzioside G
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2368538
PubChem CID	73354401
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

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

Chemical Representations

RDKit 2D 102107 0 0 0 0 0 0 0 0999 V2000 7.2346 -6.0905 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -7.2395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3062 -8.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3420 -7.2395 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -5.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5658 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -3.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -5.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5095 -4.9895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5863 -1.0950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0325 -2.5271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6567 0.4034 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1200 0.0738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3313 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6304 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9294 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6304 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3671 2.6491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8802 4.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3574 4.3191 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9160 5.2077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4290 6.6172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4648 7.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4993 8.9153 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9766 8.6549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4896 7.2453 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9407 9.8039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6842 6.8021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6139 8.7305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9062 6.8777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2760 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8578 2.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1459 3.7548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3250 2.9520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7886 4.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3518 -8.9095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3160 -10.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7932 -9.7981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -10.0586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8290 -11.4681 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3876 -10.0586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7216 -4.6809 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1213 -6.2753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4195 -8.2037 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6053 -9.1386 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3876 -7.2395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0077 -3.3366 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7316 -3.1939 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0544 -0.8318 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9466 -1.6639 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4131 -4.3361 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5453 -6.6595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7700 -6.4667 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6142 -3.4932 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9867 -4.7291 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8293 -2.9215 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3155 -4.1320 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7121 -2.0861 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4647 -0.5972 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0397 -0.7242 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5252 -2.6758 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2353 1.7873 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1371 1.1763 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5192 2.1595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2955 2.6491 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5820 5.1292 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0898 8.8398 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7917 10.7681 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9049 10.9530 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8978 7.6837 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0267 5.4539 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8333 5.8379 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6497 9.8795 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9259 8.0034 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7630 9.6946 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8278 8.3756 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1667 5.4005 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3834 7.1382 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6933 -1.9635 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1339 -2.6908 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2152 3.9150 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4291 5.0125 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2521 5.8051 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0528 -8.1595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1181 -10.9614 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7932 -11.2981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7834 -11.4681 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8648 -12.6172 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7250 -11.5202 0.0000 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 2 0 8 9 1 0 9 10 1 6 9 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 12 15 1 0 11 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 26 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 2 0 37 39 1 0 35 40 1 0 35 41 1 0 34 42 1 0 24 43 1 0 43 44 1 0 24 45 1 1 45 46 2 0 45 47 1 0 47 48 1 0 5 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 50 53 1 0 49 54 1 0 51 3 1 0 13 7 1 0 29 17 1 0 19 9 1 0 18 44 1 6 25 18 1 0 1 55 1 0 2 56 1 0 2 57 1 0 3 58 1 1 5 59 1 1 8 60 1 0 10 61 1 0 10 62 1 0 10 63 1 0 11 64 1 1 12 65 1 6 15 66 1 0 15 67 1 0 15 68 1 0 16 69 1 0 16 70 1 0 17 71 1 6 19 72 1 1 20 73 1 1 21 74 1 0 22 75 1 6 23 76 1 0 25 77 1 6 26 78 1 1 33 79 1 0 39 80 1 0 39 81 1 0 39 82 1 0 40 83 1 0 40 84 1 0 40 85 1 0 41 86 1 0 41 87 1 0 41 88 1 0 42 89 1 0 42 90 1 0 42 91 1 0 44 92 1 0 44 93 1 0 48 94 1 0 48 95 1 0 48 96 1 0 49 97 1 6 50 98 1 1 51 99 1 6 52100 1 0 53101 1 0 54102 1 0 M END

Standard InCHIKey	YNYBTCKMNHXXGZ-FIHJRPEFSA-N
Standard InCHI	InChI=1S/C36H48O18/c1-13(33(4,5)54-15(3)38)8-20(39)53-26-28-35-12-49-36(28,32(47)48-7)29(45)25(44)27(35)34(6)10-17(21(40)14(2)16(34)9-19(35)52-30(26)46)50-31-24(43)23(42)22(41)18(11-37)51-31/h8,10,14,16,18-19,22-29,31,37,41-45H,9,11-12H2,1-7H3/b13-8+/t14-,16-,18+,19+,22+,23-,24+,25+,26+,27+,28+,29-,31+,34-,35+,36+/m0/s1
SMILES	OC[C@H]1O[C@@H](OC2=C[C@@]3(C)[C@H]([C@@H](C2=O)C)C[C@@H]2[C@@]45[C@@H]3[C@@H](O)[C@H](O)[C@@]([C@@H]5[C@H](C(=O)O2)OC(=O)/C=C(/C(OC(=O)C)(C)C)C)(OC4)C(=O)OC)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	768.28	Volume:	719.642 ? Van der Waals volume.
Dense:	1.068	LogP:	0.412 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.303 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.978 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	35.0
TPSA:	271.34 ? Topological Polar Surface Area.	H-Bond Acceptor:	18.0
H-Bond Donor:	6.0	Rings:	6.0
Heavy Atoms:	18.0

MedChem Properties

QED Drug-Likeness Score:	0.088	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.221	Fsp³:	0.75
MCE-18:	178.571 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.656	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.021 ? 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:	0.075	Promiscuous compounds:	0.337

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.832	MDCK Permeability:	-5.307
Pgp-inhibitor:	0.004	Pgp-substrate:	0.233
PAMPA:	0.896 ? 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):	0.01
20% Bioavailability (F20%):	0.023	30% Bioavailability (F30%):	0.976
50% Bioavailability (F50%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.986
Plasma Protein Binding (PPB):	69.956%	Volume Distribution (VD):	-0.262
Fu:	29.336% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.103

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	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:	0.044
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	0.11
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.022 ? 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):

1.257

Half-life (T1/2):

4.029

ADMET: Toxicity

hERG Blockers:	0.003	hERG Blockers (10um):	0.01
Human Hepatotoxicity (H-HT):	0.729	Drug-induced Liver Injury (DILI):	0.994
AMES Toxicity:	0.976	Rat Oral Acute Toxicity:	0.06
Maximum Recommended Daily Dose:	0.141	Skin Sensitization:	1.0
Carcinogencity:	0.254	Eye Corrosion:	0.0
Eye Irritation:	0.006	Respiratory Toxicity:	0.006
Drug-induced Neurotoxicity:	0.062	Ototoxicity:	0.969
Hematotoxicity:	0.471	Drug-induced Nephrotoxicity:	0.991
Genotoxicity:	0.997	RPMI-8226 Immunitoxicity:	0.289
A549 Cytotoxicity:	0.174	Hek293 Cytotoxicity:	0.465
BCF:	0.501 ? 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:	3.29 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.159 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.4 ? 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
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/0031-9422(96)00258-0]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S1383-5769(99)00023-9]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10086989]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1512598]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15165151]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	fruit	Indonesia	n.a.	PMID[17896817]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	Vietnam	n.a.	PMID[19026551]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20050684]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2089121]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22506620]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3379416]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3443857]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3760882]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3841557]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7288443]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8133299]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	xylem	n.a.	PMID[8133299]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691212]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21014	Brucea antidysenterica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14948	Brucea javanica	Species	Simaroubaceae	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
IC50	1
EC50	1
ED50	2
Inhibition	1

Activity Type	# Activity
Cell line	3
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
NPT759	Cell line	H9	Homo sapiens	IC50	=	37000.0	nM	PMID[17949976]
NPT168	Cell line	P388	Mus musculus	ED50	=	1.25	ug ml-1	PMID[8289059]
NPT137	Cell line	L1210	Mus musculus	ED50	=	2.58	ug ml-1	PMID[8289059]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	23000.0	nM	PMID[17949976]
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	33.7	%	PMID[19908867]

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 NPC471089 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	19303
0.1-0.2	27024
0.2-0.3	3428
0.3-0.4	53
0.4-0.5	15
0.5-0.6	12
0.6-0.7	9
0.7-0.8	0
0.8-0.85	4
0.85-0.9	5
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8977	High Similarity	NPC190065
0.8778	High Similarity	NPC141215
0.8681	High Similarity	NPC479019
0.8621	High Similarity	NPC475636
0.8587	High Similarity	NPC295885
0.8495	Intermediate Similarity	NPC140045
0.8242	Intermediate Similarity	NPC602216
0.8191	Intermediate Similarity	NPC54614
0.8041	Intermediate Similarity	NPC480778
0.7212	Intermediate Similarity	NPC480790
0.7087	Intermediate Similarity	NPC102465
0.6931	Remote Similarity	NPC480779
0.6634	Remote Similarity	NPC596
0.6569	Remote Similarity	NPC262813
0.6535	Remote Similarity	NPC309096
0.6321	Remote Similarity	NPC251998
0.6286	Remote Similarity	NPC480789
0.6238	Remote Similarity	NPC87662
0.6224	Remote Similarity	NPC470779
0.6061	Remote Similarity	NPC480786
0.5842	Remote Similarity	NPC105926
0.58	Remote Similarity	NPC480777
0.5741	Remote Similarity	NPC295220
0.567	Remote Similarity	NPC476008
0.5464	Remote Similarity	NPC479018
0.5354	Remote Similarity	NPC146432
0.5354	Remote Similarity	NPC470778
0.5347	Remote Similarity	NPC480787
0.5312	Remote Similarity	NPC213084
0.5152	Remote Similarity	NPC89929
0.5049	Remote Similarity	NPC480785
0.5049	Remote Similarity	NPC480784

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC471089 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7164
0.1-0.2	1929
0.2-0.3	57
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