NPASS Compound

Natural Product: NPC113978

Natural Product ID	NPC113978
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BIOOLEHEEDQHNH-QXTLHTQPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL254954
PubChem CID	24770659
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols and derivatives

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 82 86 0 0 0 0 0 0 0 0999 V2000 6.8913 1.6994 -1.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5672 1.3771 -0.2882 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9430 0.2572 0.0266 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6114 -0.0876 1.4092 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0971 -0.2526 1.6076 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5279 -1.3174 0.7550 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1685 -2.6843 1.0546 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 -1.5295 0.7600 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5408 -1.8584 2.1598 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4170 -0.8230 2.3343 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1170 -0.7786 0.9527 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7474 -2.1177 0.6414 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0257 0.3568 0.6206 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1437 0.3356 1.6226 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4120 0.9601 1.1435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8278 0.1605 -0.0978 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2366 0.3369 -0.4726 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9802 -1.0015 -0.4972 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9218 1.1561 0.6353 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5180 1.0340 -1.7521 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4939 0.8932 -2.8136 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3736 -0.0817 -2.4622 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8188 0.4368 -1.1554 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0594 1.6837 -1.2642 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4237 0.3314 -0.7999 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4706 -0.2579 -1.7543 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6819 -1.0340 -1.2680 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1576 -0.5929 0.1101 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5453 0.8314 -0.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7797 -1.3828 -2.4241 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7671 2.4060 -1.5098 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9395 2.3098 0.8103 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7396 2.4023 -1.7078 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0327 2.1130 -2.2645 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1972 0.7273 -2.1876 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6727 -0.4228 -0.7748 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1945 -0.9068 1.8343 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8646 0.8064 2.0538 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7053 0.7589 1.4356 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9862 -0.4312 2.6975 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8274 -1.1427 -0.3234 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5008 -3.1756 1.7921 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1510 -2.6063 1.5138 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1489 -3.3275 0.1489 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9263 -2.5320 0.2003 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3064 -1.7571 2.9279 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0461 -2.8453 2.2116 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8179 0.1375 2.6995 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3598 -1.1757 3.0185 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3396 -2.4110 1.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0311 -2.9267 0.4895 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4227 -2.0914 -0.2203 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4768 1.3037 0.8121 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8426 0.8853 2.5618 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3677 -0.6961 1.9404 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3772 2.0299 0.9663 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1784 0.7873 1.9398 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6736 -0.9160 0.2171 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3729 -1.2186 -1.5257 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2861 -1.8207 -0.1542 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8402 -1.0284 0.1717 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1559 0.5415 1.5106 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9215 1.4315 0.1856 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4104 2.0959 0.8303 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4932 0.6547 -2.1818 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9825 1.8791 -2.9648 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9283 0.6481 -3.8186 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6103 0.0721 -3.2811 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1074 2.5044 -0.5543 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7400 2.0393 -2.2879 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0577 -0.9382 -2.4431 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0808 0.5333 -2.4630 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4845 -2.1281 -1.3108 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5819 -0.8913 -1.9367 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8213 1.3037 -0.7552 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5011 0.8746 -0.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5337 1.4231 0.9183 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4587 -1.5127 -3.1534 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7194 2.6114 -1.4671 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5492 3.1299 0.3753 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0204 2.6882 1.2963 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5831 1.7536 1.5151 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 6 11 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 17 19 1 0 17 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 6 25 24 1 6 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 6 22 30 1 0 20 31 1 0 2 32 1 0 28 8 1 0 28 11 1 0 25 13 1 0 23 16 1 0 25 23 1 0 1 33 1 0 1 34 1 0 1 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 6 41 1 6 7 42 1 0 7 43 1 0 7 44 1 0 8 45 1 6 9 46 1 0 9 47 1 0 10 48 1 0 10 49 1 0 12 50 1 0 12 51 1 0 12 52 1 0 13 53 1 6 14 54 1 0 14 55 1 0 15 56 1 0 15 57 1 0 16 58 1 1 18 59 1 0 18 60 1 0 18 61 1 0 19 62 1 0 19 63 1 0 19 64 1 0 20 65 1 6 21 66 1 0 21 67 1 0 22 68 1 6 24 69 1 0 24 70 1 0 26 71 1 0 26 72 1 0 27 73 1 0 27 74 1 0 29 75 1 0 29 76 1 0 29 77 1 0 30 78 1 0 31 79 1 0 32 80 1 0 32 81 1 0 32 82 1 0 M END

Standard InCHIKey	BIOOLEHEEDQHNH-QXTLHTQPSA-N
Standard InCHI	InChI=1S/C30H50O2/c1-19(2)9-8-10-20(3)21-13-14-28(7)23-12-11-22-26(4,5)24(31)17-25(32)30(22)18-29(23,30)16-15-27(21,28)6/h9,20-25,31-32H,8,10-18H2,1-7H3/t20-,21-,22+,23+,24+,25+,27-,28+,29+,30-/m1/s1
SMILES	CC(=CCC[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)[C@H](C[C@@H]([C@]54C[C@@]35CC[C@]12C)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	442.38	Volume:	499.598 ? Van der Waals volume.
Dense:	0.885	LogP:	5.246 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.197 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.055 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	23.0
TPSA:	40.46 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	5.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.454	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.704	Fsp³:	0.933
MCE-18:	133.966 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.685	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? 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:	0.444	Promiscuous compounds:	0.246

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.1	MDCK Permeability:	-4.925
Pgp-inhibitor:	0.008	Pgp-substrate:	0.128
PAMPA:	0.753 ? 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):	0.002
20% Bioavailability (F20%):	0.051	30% Bioavailability (F30%):	0.281
50% Bioavailability (F50%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.252	MRP1:	0.046
Plasma Protein Binding (PPB):	96.564%	Volume Distribution (VD):	0.203
Fu:	3.959% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.838
BSEP inhibitor:	0.019

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.989	CYP2C19-substrate:	0.003
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.004
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	0.997
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.813
HLM stability:	0.842 ? 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):

15.017

Half-life (T1/2):

1.354

ADMET: Toxicity

hERG Blockers:	0.147	hERG Blockers (10um):	0.463
Human Hepatotoxicity (H-HT):	0.494	Drug-induced Liver Injury (DILI):	0.026
AMES Toxicity:	0.223	Rat Oral Acute Toxicity:	0.489
Maximum Recommended Daily Dose:	0.597	Skin Sensitization:	0.924
Carcinogencity:	0.799	Eye Corrosion:	0.009
Eye Irritation:	0.49	Respiratory Toxicity:	0.943
Drug-induced Neurotoxicity:	0.082	Ototoxicity:	0.668
Hematotoxicity:	0.448	Drug-induced Nephrotoxicity:	0.587
Genotoxicity:	0.132	RPMI-8226 Immunitoxicity:	0.077
A549 Cytotoxicity:	0.383	Hek293 Cytotoxicity:	0.146
BCF:	2.762 ? 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:	5.19 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.105 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.113 ? 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
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	roots	northern Saudi desert	n.a.	PMID[10924184]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18177010]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9036	Dipteryx lacunifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9883	Allium giganteum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10085	Aspergillus varians	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3693	Calpurnia aurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29336	Corynandra chelidonii	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4463	Cytisus canariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6022	Cytisus supinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24891	Elmerina caryae	Species	Aporpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5284	Ramalina hierrensis	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9639	Prunus puddum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8810	Pinus austriaca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2328	Lagochilus setulosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1586	Gorgonocephalus chilensis	Species	Gorgonocephalidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8985	Gazania rigens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5886	Fossombronia alaskana	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10085	Aspergillus varians	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2328	Lagochilus setulosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7260	Angelica genuflexa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8985	Gazania rigens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24891	Elmerina caryae	Species	Aporpiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5284	Ramalina hierrensis	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1586	Gorgonocephalus chilensis	Species	Gorgonocephalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8810	Pinus austriaca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29336	Corynandra chelidonii	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO817	Dictamnus angustifolius	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9036	Dipteryx lacunifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6022	Cytisus supinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4463	Cytisus canariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9639	Prunus puddum	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3693	Calpurnia aurea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9883	Allium giganteum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11707	Ruta chalepensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6831	Commiphora opobalsamum	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5886	Fossombronia alaskana	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8297	Hydnellum caeruleum	Species	Thelephoraceae	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	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
NPT306	Cell line	PC-3	Homo sapiens	IC50	>	50000.0	nM	PMID[18177010]
NPT90	Cell line	DU-145	Homo sapiens	IC50	>	50000.0	nM	PMID[18177010]

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 NPC113978 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	25882
0.1-0.2	21292
0.2-0.3	2353
0.3-0.4	238
0.4-0.5	61
0.5-0.6	18
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	0

Similarity Score	Similarity Level	Natural Product ID
0.7358	Intermediate Similarity	NPC269058
0.7358	Intermediate Similarity	NPC71520
0.7115	Intermediate Similarity	NPC85346
0.7115	Intermediate Similarity	NPC65897
0.7115	Intermediate Similarity	NPC80237
0.6032	Remote Similarity	NPC300179
0.5965	Remote Similarity	NPC302041
0.5932	Remote Similarity	NPC89747
0.5758	Remote Similarity	NPC289670
0.5625	Remote Similarity	NPC102426
0.5439	Remote Similarity	NPC331618
0.5439	Remote Similarity	NPC257191
0.5424	Remote Similarity	NPC275671
0.5345	Remote Similarity	NPC604180
0.5263	Remote Similarity	NPC607543
0.5254	Remote Similarity	NPC214770
0.5254	Remote Similarity	NPC477856
0.5246	Remote Similarity	NPC139206
0.5172	Remote Similarity	NPC196358
0.5152	Remote Similarity	NPC283733
0.5088	Remote Similarity	NPC41577
0.5085	Remote Similarity	NPC200243
0.5085	Remote Similarity	NPC254509
0.5085	Remote Similarity	NPC82623

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC113978 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8189
0.1-0.2	923
0.2-0.3	38
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