NPASS Compound

Natural Product: NPC267539

Natural Product ID	NPC267539
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gentiside C
IUPAC Name	[(14S)-14-methylhexadecyl] 2,3-dihydroxybenzoate
Synonyms	Gentiside C
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1254184
PubChem CID	46899083
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001350] Benzoic acid esters [CHEMONTID:0004699] m-Hydroxybenzoic acid esters

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 68 68 0 0 0 0 0 0 0 0999 V2000 -6.3400 -1.3867 1.4668 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7912 -0.0213 1.8701 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1200 0.9300 0.7858 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0609 1.3179 -0.1636 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4106 0.2658 -0.9811 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3756 0.8619 -1.9412 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2930 1.5962 -1.2371 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4807 0.7717 -0.2693 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8030 -0.3858 -0.9571 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9430 -1.2072 -0.1032 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3758 -0.8596 0.3776 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7949 0.3771 1.0177 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9774 1.6013 0.1687 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0894 1.3683 -0.8675 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4151 1.0582 -0.2099 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4079 0.8597 -1.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6979 0.5630 -0.9063 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0955 -0.5134 -0.1514 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2089 -1.3304 0.1993 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4687 -0.7573 0.2599 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5059 0.0793 -0.0750 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7889 -0.1991 0.3411 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0997 -1.3126 1.1034 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0573 -2.1519 1.4391 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7697 -1.8658 1.0173 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7599 -2.7477 1.3860 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3619 -3.2704 2.2034 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4049 0.4987 0.0723 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6475 -1.7020 0.4526 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2625 -1.5329 1.6908 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8748 -2.1335 2.1374 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9834 0.4263 2.5053 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6633 -0.1336 2.5824 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4406 1.8944 1.3069 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2860 1.8975 0.4382 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4809 2.0735 -0.9023 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1376 -0.2963 -1.5643 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8551 -0.4428 -0.3120 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9979 0.0995 -2.6392 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9383 1.5963 -2.5528 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5793 1.9645 -2.0037 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7022 2.4716 -0.7003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2032 0.3280 0.5219 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8435 1.3959 0.3148 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2254 0.0682 -1.8118 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5720 -1.0290 -1.4797 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8657 -2.2554 -0.6232 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5536 -1.5653 0.8301 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6566 -1.7063 1.1377 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1234 -1.1464 -0.4675 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0234 0.6451 1.8082 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7855 0.2592 1.5706 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1902 2.4938 0.7760 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0993 1.8093 -0.4309 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7468 0.5115 -1.4819 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1900 2.2352 -1.5345 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3245 0.0414 0.2743 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7128 1.8194 0.5149 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9759 0.1575 -2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4619 1.8526 -1.8671 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2553 0.9490 -0.6719 H 0 0 0 0 0 0 0 0 0 0 0 0 10.6025 0.4531 0.0809 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1169 -1.5250 1.4280 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3640 -3.3227 0.6488 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7823 -4.0518 1.6796 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4937 1.1085 -0.8377 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2771 0.7255 0.7202 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3795 -0.5736 -0.1843 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 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 24 27 1 0 3 28 1 0 25 20 1 0 1 29 1 0 1 30 1 0 1 31 1 0 2 32 1 0 2 33 1 0 3 34 1 1 4 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 6 40 1 0 7 41 1 0 7 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 10 47 1 0 10 48 1 0 11 49 1 0 11 50 1 0 12 51 1 0 12 52 1 0 13 53 1 0 13 54 1 0 14 55 1 0 14 56 1 0 15 57 1 0 15 58 1 0 16 59 1 0 16 60 1 0 21 61 1 0 22 62 1 0 23 63 1 0 26 64 1 0 27 65 1 0 28 66 1 0 28 67 1 0 28 68 1 0 M END

Standard InCHIKey	XGXUFBAHOWHDNU-FQEVSTJZSA-N
Standard InCHI	InChI=1S/C24H40O4/c1-3-20(2)16-13-11-9-7-5-4-6-8-10-12-14-19-28-24(27)21-17-15-18-22(25)23(21)26/h15,17-18,20,25-26H,3-14,16,19H2,1-2H3/t20-/m0/s1
SMILES	CC[C@@H](CCCCCCCCCCCCCOC(=O)c1cccc(c1O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	392.29	Volume:	439.719 ? Van der Waals volume.
Dense:	0.892	LogP:	7.755 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.105 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.461 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	17.0	Rigid Bonds:	7.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.181	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.659	Fsp³:	0.708
MCE-18:	16.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.679	Fluc inhibitor:	0.486 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.093 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.116 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.754	Promiscuous compounds:	0.33

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.109	MDCK Permeability:	-4.766
Pgp-inhibitor:	0.0	Pgp-substrate:	0.007
PAMPA:	0.001 ? 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):	0.29
20% Bioavailability (F20%):	0.977	30% Bioavailability (F30%):	0.993
50% Bioavailability (F50%):	0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	0.994
Plasma Protein Binding (PPB):	97.699%	Volume Distribution (VD):	0.219
Fu:	1.765% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.839
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.369
BSEP inhibitor:	0.327

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.975
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.892
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.236
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.675
CYP3A4-inhibitor:	0.746	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.964 ? 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):

5.931

Half-life (T1/2):

0.711

ADMET: Toxicity

hERG Blockers:	0.353	hERG Blockers (10um):	0.89
Human Hepatotoxicity (H-HT):	0.088	Drug-induced Liver Injury (DILI):	0.086
AMES Toxicity:	0.049	Rat Oral Acute Toxicity:	0.095
Maximum Recommended Daily Dose:	0.164	Skin Sensitization:	0.992
Carcinogencity:	0.649	Eye Corrosion:	0.737
Eye Irritation:	0.998	Respiratory Toxicity:	0.746
Drug-induced Neurotoxicity:	0.008	Ototoxicity:	0.111
Hematotoxicity:	0.005	Drug-induced Nephrotoxicity:	0.018
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.055
A549 Cytotoxicity:	0.83	Hek293 Cytotoxicity:	0.403
BCF:	0.748 ? 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:	4.528 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.239 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.832 ? 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
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	roots	n.a.	n.a.	PMID[17375953]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20813533]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	stem	n.a.	PMID[21043460]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21043460]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21043460]
NPO27624	Swartzia simplex	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26654828]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32372353]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33588649]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37849964]
NPO12009	Abies pinsapo	Species	Pinaceae	Eukaryota	Wood	n.a.	n.a.	PMID[7931362]
NPO17054	Streptomyces gardneri	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15518	Streptomyces netropsis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17699	Solanum glaucophyllum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16817	Aglaia argentea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16958	Jurinea albicaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16817	Aglaia argentea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16958	Jurinea albicaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13251	Iris nertchinskia	Species	Tarachodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16817	Aglaia argentea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18843	Antirrhinum majus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18372	Lobophytum crassospiculatum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18511	Latimeria chalumnae	Species	Coelacanthidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17699	Solanum glaucophyllum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17493	Alstonia spatulata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16073	Sarcomelicope megistophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27624	Swartzia simplex	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17368	Erythrina senegalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12009	Abies pinsapo	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19120	Strychnos aculeata	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15856	Podocarpus hallii	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15518	Streptomyces netropsis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17711	Sphenoclea zeylanica	Species	Sphenocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16646	Artemisia campestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14721	Dentitheca habereri	Species	Plumulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18234	Gentiana rigescens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3046	Schisandra bicolor	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17054	Streptomyces gardneri	Species	Streptomycetaceae	Bacteria	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
Activity	2

Activity Type	# Activity
Cell line	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
NPT681	Cell line	PC-12	Rattus norvegicus	Activity	=	67.0	%	PMID[20813533]
NPT681	Cell line	PC-12	Rattus norvegicus	Activity	=	91.0	%	PMID[20813533]

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 NPC267539 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	8897
0.1-0.2	38583
0.2-0.3	2291
0.3-0.4	57
0.4-0.5	16
0.5-0.6	3
0.6-0.7	0
0.7-0.8	0
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC71108
1.0	High Similarity	NPC204257
1.0	High Similarity	NPC229638
1.0	High Similarity	NPC176102
0.8696	High Similarity	NPC254832
0.8696	High Similarity	NPC29317
0.8043	Intermediate Similarity	NPC295406
0.8043	Intermediate Similarity	NPC200422
0.8043	Intermediate Similarity	NPC289572
0.8043	Intermediate Similarity	NPC157478
0.5385	Remote Similarity	NPC90522
0.5294	Remote Similarity	NPC607895
0.5098	Remote Similarity	NPC603245

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC267539 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2136
0.1-0.2	6707
0.2-0.3	298
0.3-0.4	7
0.4-0.5	2
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