NPASS Compound

Natural Product: NPC61530

Natural Product ID	NPC61530
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NDYMQXYDSVBNLL-GPIPDBLZSA-M
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	25245182
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001686] Cucurbitacins

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 83 86 0 0 0 0 0 0 0 0999 V2000 8.4406 -0.4869 0.5703 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1615 -1.1108 1.0624 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1516 -2.3201 1.3635 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0059 -0.3880 1.1893 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7712 -0.9044 1.6428 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3783 -2.0082 0.6861 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9600 -1.4900 3.0039 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7824 0.2049 1.6308 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2397 0.6616 0.5135 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2686 1.7508 0.5013 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9702 2.2478 1.6240 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6956 2.2136 -0.7862 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8931 2.7664 -1.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1434 1.0987 -1.5406 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5535 1.4224 -2.8918 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6074 0.4629 -3.1149 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1160 0.2784 -1.7247 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9122 1.5026 -1.3956 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0535 -0.9077 -1.5462 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3749 -0.6710 -2.2352 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3633 0.0363 -1.3936 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4917 -0.3186 -0.1272 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6401 -1.3943 0.3478 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7288 -1.7304 1.7613 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7593 -1.3570 2.4759 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8470 -0.5882 1.8584 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0172 -0.7243 2.2334 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4597 0.3464 0.7748 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6572 0.8789 0.0189 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8219 1.5620 1.4605 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8483 -1.6836 3.8507 O 0 0 0 0 0 1 0 0 0 0 0 0 -2.1810 -1.3289 -0.1234 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7018 -2.7750 0.1065 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4755 -0.4018 0.8072 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8929 -0.2271 1.9539 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2441 0.3829 0.4751 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1623 0.1612 -0.9319 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7683 -1.2309 -0.9966 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2619 2.7371 -3.1141 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9083 3.2936 -0.5083 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4433 0.5897 0.8282 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4069 -0.5834 -0.5350 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3224 -0.9561 1.0132 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6727 -1.8088 -0.3466 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9185 -2.9236 1.0221 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2990 -2.2339 0.8066 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2306 -2.5562 3.0147 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0158 -1.3845 3.5864 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7445 -0.9547 3.5938 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5191 0.6316 2.5885 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5558 0.1876 -0.4295 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4722 3.3661 -0.8304 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5329 1.9401 -1.9101 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5782 3.4515 -2.3630 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0886 0.5091 -1.8100 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2526 1.1542 -3.7479 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2493 -0.5146 -3.4861 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3724 0.9056 -3.7813 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4009 2.4690 -1.5609 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7083 1.5787 -2.2000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3491 1.5502 -0.4044 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6100 -1.7406 -2.1239 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1567 -0.1413 -3.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8620 -1.6260 -2.5319 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9554 0.8241 -1.8335 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0220 -2.3323 -0.1958 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9437 -2.2922 2.2320 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3829 1.2358 0.7696 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3246 1.7425 -0.5826 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1517 0.1159 -0.6014 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1806 1.2585 2.3014 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3542 2.2368 0.7387 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6953 2.1128 1.9161 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5002 -3.4396 0.4891 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3612 -3.2442 -0.8383 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9254 -2.7697 0.8926 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4661 1.4300 0.7394 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5338 -0.0238 1.1514 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9598 -1.6614 0.0091 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3436 -1.8964 -1.7364 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8464 -1.1448 -1.3733 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4420 2.8110 -3.7926 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3547 4.1657 -0.5667 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 5 7 1 0 5 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 26 28 1 0 28 29 1 0 28 30 1 0 25 31 1 0 23 32 1 0 32 33 1 6 32 34 1 0 34 35 2 0 34 36 1 0 36 37 1 0 37 38 1 1 15 39 1 0 12 40 1 1 37 14 1 0 37 17 1 0 32 19 1 0 28 22 1 0 1 41 1 0 1 42 1 0 1 43 1 0 6 44 1 0 6 45 1 0 6 46 1 0 7 47 1 0 7 48 1 0 7 49 1 0 8 50 1 0 9 51 1 0 13 52 1 0 13 53 1 0 13 54 1 0 14 55 1 0 15 56 1 6 16 57 1 0 16 58 1 0 18 59 1 0 18 60 1 0 18 61 1 0 19 62 1 0 20 63 1 0 20 64 1 0 21 65 1 0 23 66 1 0 24 67 1 0 29 68 1 0 29 69 1 0 29 70 1 0 30 71 1 0 30 72 1 0 30 73 1 0 33 74 1 0 33 75 1 0 33 76 1 0 36 77 1 0 36 78 1 0 38 79 1 0 38 80 1 0 38 81 1 0 39 82 1 0 40 83 1 0 M CHG 1 31 -1 M END

Standard InCHIKey	NDYMQXYDSVBNLL-GPIPDBLZSA-M
Standard InCHI	InChI=1S/C32H44O8/c1-17(33)40-27(2,3)13-12-23(36)32(9,39)25-21(35)15-29(6)22-11-10-18-19(14-20(34)26(38)28(18,4)5)31(22,8)24(37)16-30(25,29)7/h10,12-14,19,21-22,25,34-35,39H,11,15-16H2,1-9H3/p-1/b13-12+/t19?,21-,22?,25?,29+,30-,31+,32+/m1/s1
SMILES	CC(=O)OC(C)(C)/C=C/C(=O)[C@@](C)(C1[C@@H](C[C@@]2(C)C3CC=C4C(C=C(C(=O)C4(C)C)[O-])[C@]3(C)C(=O)C[C@]12C)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	556.3	Volume:	579.669 ? Van der Waals volume.
Dense:	0.96	LogP:	1.749 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.813 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.977 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	25.0
TPSA:	138.2 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	3.0	Rings:	4.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.26	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.33	Fsp³:	0.688
MCE-18:	96.296 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.177	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.175 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.111 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.273	Promiscuous compounds:	0.2

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.982	MDCK Permeability:	-4.661
Pgp-inhibitor:	0.298	Pgp-substrate:	0.017
PAMPA:	0.969 ? 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):	0.009
20% Bioavailability (F20%):	0.801	30% Bioavailability (F30%):	0.969
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.995
Plasma Protein Binding (PPB):	89.387%	Volume Distribution (VD):	0.036
Fu:	11.756% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.045
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.983	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? 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):

2.236

Half-life (T1/2):

1.422

ADMET: Toxicity

hERG Blockers:	0.007	hERG Blockers (10um):	0.088
Human Hepatotoxicity (H-HT):	0.7	Drug-induced Liver Injury (DILI):	0.799
AMES Toxicity:	0.316	Rat Oral Acute Toxicity:	0.686
Maximum Recommended Daily Dose:	0.783	Skin Sensitization:	0.932
Carcinogencity:	0.663	Eye Corrosion:	0.0
Eye Irritation:	0.021	Respiratory Toxicity:	0.652
Drug-induced Neurotoxicity:	0.177	Ototoxicity:	0.503
Hematotoxicity:	0.212	Drug-induced Nephrotoxicity:	0.712
Genotoxicity:	0.994	RPMI-8226 Immunitoxicity:	0.178
A549 Cytotoxicity:	0.413	Hek293 Cytotoxicity:	0.585
BCF:	0.554 ? 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:	3.38 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.172 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.542 ? 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
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2004.07.004]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2005.08.001]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12379786]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[14993759]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Stems	n.a.	n.a.	PMID[19348465]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23507362]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27128895]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	Resinous Wood	n.a.	n.a.	PMID[29227647]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	Fruit juice	n.a.	n.a.	PMID[3404148]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38792158]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8111	Rhizoma bolbostemmae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed Oil	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8111	Rhizoma bolbostemmae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO13450	Cucumis melo	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24328	Gratiola officinalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24454	Begonia nantoensis	Species	Begoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3344	Bryonia alba	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14558	Aquilaria sinensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13450	Cucumis melo	Species	Cucurbitaceae	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 NPC61530 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	19277
0.1-0.2	28780
0.2-0.3	1725
0.3-0.4	33
0.4-0.5	26
0.5-0.6	10
0.6-0.7	7
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
0.7361	Intermediate Similarity	NPC221144
0.6905	Remote Similarity	NPC213634
0.6892	Remote Similarity	NPC100267
0.6892	Remote Similarity	NPC475524
0.6667	Remote Similarity	NPC257457
0.6667	Remote Similarity	NPC482855
0.6667	Remote Similarity	NPC311554
0.6076	Remote Similarity	NPC239273
0.5526	Remote Similarity	NPC111323
0.5455	Remote Similarity	NPC152091
0.5432	Remote Similarity	NPC148458
0.5422	Remote Similarity	NPC488451
0.5309	Remote Similarity	NPC484814
0.5244	Remote Similarity	NPC304495
0.5244	Remote Similarity	NPC486329
0.5195	Remote Similarity	NPC87351
0.5181	Remote Similarity	NPC475294
0.5128	Remote Similarity	NPC311612

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC61530 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6906
0.1-0.2	2201
0.2-0.3	43
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