NPASS Compound

Natural Product: NPC211386

Natural Product ID	NPC211386
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(3R,4R)-4-[(3,4-Dimethoxyphenyl)Methyl]-3-[(3,4,5-Trimethoxyphenyl)Methyl]Oxolan-2-One
IUPAC Name	(3R,4R)-4-[(3,4-dimethoxyphenyl)methyl]-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1990222
PubChem CID	384878
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

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 58 60 0 0 0 0 0 0 0 0999 V2000 6.0082 1.3180 3.2564 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9987 1.7092 2.3471 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3721 0.7958 1.5119 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6950 -0.5632 1.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0677 -1.4673 0.6795 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0737 -1.0519 -0.2072 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4091 -2.0131 -1.0977 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1942 -2.6704 -0.5731 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3757 -3.4765 0.6806 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0907 -3.4984 1.2718 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7764 -2.5996 0.6600 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0337 -2.5656 0.9166 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0311 -1.7858 -0.2565 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6651 -1.2955 -1.4858 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8204 -0.4333 -1.2862 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0985 -0.9472 -1.2524 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1926 -0.1305 -1.0492 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0757 1.2351 -0.8696 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8041 1.7546 -0.9024 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7132 0.9449 -1.1045 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6442 3.1157 -0.7267 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4252 3.7999 -0.7292 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2142 2.0178 -0.6672 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5970 2.1723 0.6980 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4564 -0.6980 -1.0231 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6239 -2.0863 -1.2003 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7604 0.2867 -0.2038 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3923 1.1958 0.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0183 2.5522 0.5815 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0105 2.9836 -0.3165 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7421 0.6274 2.7746 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4920 2.2298 3.6602 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5086 0.7077 4.0585 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4685 -0.8595 2.2096 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3752 -2.5047 0.7362 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1095 -2.8295 -1.4268 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1317 -1.4959 -2.0457 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8060 -3.4078 -1.3415 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6211 -4.5419 0.4382 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1553 -3.1213 1.3556 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3314 -0.8724 0.3140 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9753 -2.1860 -2.0707 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0586 -0.7520 -2.1384 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2855 -2.0266 -1.3989 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7105 1.3571 -1.1315 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9424 3.7157 0.2796 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6973 3.4160 -1.4711 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5337 4.8856 -0.9296 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8577 1.1865 1.1549 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7094 2.5306 1.2686 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4211 2.8967 0.8169 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1708 -2.6624 -0.3725 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7290 -2.2662 -1.1806 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2279 -2.4427 -2.1717 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9798 0.6289 -0.8962 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2051 2.6726 -1.3514 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8393 4.0544 -0.1776 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0797 2.4608 0.0090 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 18 23 1 0 23 24 1 0 17 25 1 0 25 26 1 0 6 27 1 0 27 28 2 0 28 29 1 0 29 30 1 0 28 3 1 0 13 8 1 0 20 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 4 34 1 0 5 35 1 0 7 36 1 0 7 37 1 0 8 38 1 6 9 39 1 0 9 40 1 0 13 41 1 1 14 42 1 0 14 43 1 0 16 44 1 0 20 45 1 0 22 46 1 0 22 47 1 0 22 48 1 0 24 49 1 0 24 50 1 0 24 51 1 0 26 52 1 0 26 53 1 0 26 54 1 0 27 55 1 0 30 56 1 0 30 57 1 0 30 58 1 0 M END

Standard InCHIKey	QFFURUDOUPSWTF-DLBZAZTESA-N
Standard InCHI	InChI=1S/C23H28O7/c1-25-18-7-6-14(10-19(18)26-2)8-16-13-30-23(24)17(16)9-15-11-20(27-3)22(29-5)21(12-15)28-4/h6-7,10-12,16-17H,8-9,13H2,1-5H3/t16-,17+/m0/s1
SMILES	COc1ccc(C[C@H]2COC(=O)[C@@H]2Cc2cc(c(c(c2)OC)OC)OC)cc1OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	416.18	Volume:	423.771 ? Van der Waals volume.
Dense:	0.982	LogP:	1.891 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.247 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.598 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	18.0
TPSA:	72.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	0.0	Rings:	3.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.581	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.094	Fsp³:	0.435
MCE-18:	60.455 ? 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:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.139	Fluc inhibitor:	0.158 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.028 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.336 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.298	Promiscuous compounds:	0.102

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.63	MDCK Permeability:	-4.617
Pgp-inhibitor:	0.695	Pgp-substrate:	0.152
PAMPA:	0.012 ? 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):	0.003
20% Bioavailability (F20%):	0.335	30% Bioavailability (F30%):	0.074
50% Bioavailability (F50%):	0.501

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.023	MRP1:	0.974
Plasma Protein Binding (PPB):	96.43%	Volume Distribution (VD):	-0.358
Fu:	2.742% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.984
OATP1B3 inhibitor:	0.959	BCRP inhibitor:	0.045
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.007	CYP1A2-substrate:	0.686
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	0.003	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.99
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.715 ? 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):

6.396

Half-life (T1/2):

1.675

ADMET: Toxicity

hERG Blockers:	0.341	hERG Blockers (10um):	0.644
Human Hepatotoxicity (H-HT):	0.934	Drug-induced Liver Injury (DILI):	0.983
AMES Toxicity:	0.569	Rat Oral Acute Toxicity:	0.585
Maximum Recommended Daily Dose:	0.545	Skin Sensitization:	0.947
Carcinogencity:	0.746	Eye Corrosion:	0.002
Eye Irritation:	0.613	Respiratory Toxicity:	0.574
Drug-induced Neurotoxicity:	0.946	Ototoxicity:	0.781
Hematotoxicity:	0.826	Drug-induced Nephrotoxicity:	0.945
Genotoxicity:	0.977	RPMI-8226 Immunitoxicity:	0.282
A549 Cytotoxicity:	0.404	Hek293 Cytotoxicity:	0.52
BCF:	1.692 ? 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:	4.162 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.511 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.883 ? 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
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679319]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31096694]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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
GI50	59

Activity Type	# Activity
Cell line	59

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
NPT368	Cell line	SN12C	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT367	Cell line	MDA-N	Homo sapiens	GI50	n.a.	78704.58	nM	PubChem BioAssay data set
NPT370	Cell line	NCI-H23	Homo sapiens	GI50	n.a.	99311.6	nM	PubChem BioAssay data set
NPT369	Cell line	ACHN	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT371	Cell line	UO-31	Homo sapiens	GI50	n.a.	43551.19	nM	PubChem BioAssay data set
NPT372	Cell line	HOP-92	Homo sapiens	GI50	n.a.	15958.79	nM	PubChem BioAssay data set
NPT90	Cell line	DU-145	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT116	Cell line	HL-60	Homo sapiens	GI50	n.a.	9727.47	nM	PubChem BioAssay data set
NPT374	Cell line	SF-539	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT373	Cell line	SK-MEL-5	Homo sapiens	GI50	n.a.	26242.19	nM	PubChem BioAssay data set
NPT375	Cell line	Malme-3M	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT111	Cell line	K562	Homo sapiens	GI50	n.a.	77803.66	nM	PubChem BioAssay data set
NPT377	Cell line	OVCAR-3	Homo sapiens	GI50	n.a.	89125.09	nM	PubChem BioAssay data set
NPT112	Cell line	MOLT-4	Homo sapiens	GI50	n.a.	32433.96	nM	PubChem BioAssay data set
NPT379	Cell line	HOP-62	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT378	Cell line	NCI/ADR-RES	Homo sapiens	GI50	n.a.	41114.97	nM	PubChem BioAssay data set
NPT380	Cell line	U-251	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT381	Cell line	OVCAR-8	Homo sapiens	GI50	n.a.	50118.72	nM	PubChem BioAssay data set
NPT382	Cell line	OVCAR-5	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT82	Cell line	MDA-MB-231	Homo sapiens	GI50	n.a.	87297.14	nM	PubChem BioAssay data set
NPT383	Cell line	SNB-19	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT384	Cell line	TK-10	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT385	Cell line	SR	Homo sapiens	GI50	n.a.	5902.01	nM	PubChem BioAssay data set
NPT323	Cell line	SW-620	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT386	Cell line	KM12	Homo sapiens	GI50	n.a.	70307.23	nM	PubChem BioAssay data set
NPT455	Cell line	NCI-H522	Homo sapiens	GI50	n.a.	68706.84	nM	PubChem BioAssay data set
NPT387	Cell line	M14	Homo sapiens	GI50	n.a.	90364.95	nM	PubChem BioAssay data set
NPT388	Cell line	NCI-H322M	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT389	Cell line	RPMI-8226	Homo sapiens	GI50	n.a.	17100.15	nM	PubChem BioAssay data set
NPT390	Cell line	LOX IMVI	Homo sapiens	GI50	n.a.	74131.02	nM	PubChem BioAssay data set
NPT456	Cell line	OVCAR-4	Homo sapiens	GI50	n.a.	61659.5	nM	PubChem BioAssay data set
NPT457	Cell line	BT-549	Homo sapiens	GI50	n.a.	31988.95	nM	PubChem BioAssay data set
NPT147	Cell line	SK-MEL-2	Homo sapiens	GI50	n.a.	88307.99	nM	PubChem BioAssay data set
NPT81	Cell line	A549	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT391	Cell line	HCC 2998	Homo sapiens	GI50	n.a.	81658.24	nM	PubChem BioAssay data set
NPT392	Cell line	SNB-75	Homo sapiens	GI50	n.a.	67764.15	nM	PubChem BioAssay data set
NPT148	Cell line	HCT-15	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT393	Cell line	HCT-116	Homo sapiens	GI50	n.a.	87902.25	nM	PubChem BioAssay data set
NPT395	Cell line	SF-268	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT394	Cell line	EKVX	Homo sapiens	GI50	n.a.	65765.78	nM	PubChem BioAssay data set
NPT306	Cell line	PC-3	Homo sapiens	GI50	n.a.	41975.9	nM	PubChem BioAssay data set
NPT83	Cell line	MCF7	Homo sapiens	GI50	n.a.	63973.48	nM	PubChem BioAssay data set
NPT146	Cell line	SK-OV-3	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT396	Cell line	T47D	Homo sapiens	GI50	n.a.	17864.88	nM	PubChem BioAssay data set
NPT397	Cell line	NCI-H460	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT308	Cell line	CAKI-1	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT398	Cell line	UACC-62	Homo sapiens	GI50	n.a.	72110.75	nM	PubChem BioAssay data set
NPT400	Cell line	MDA-MB-435	Homo sapiens	GI50	n.a.	81096.11	nM	PubChem BioAssay data set
NPT399	Cell line	SF-295	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT458	Cell line	IGROV-1	Homo sapiens	GI50	n.a.	94623.72	nM	PubChem BioAssay data set
NPT401	Cell line	786-0	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT402	Cell line	Hs-578T	Homo sapiens	GI50	n.a.	38018.94	nM	PubChem BioAssay data set
NPT403	Cell line	UACC-257	Homo sapiens	GI50	n.a.	74989.42	nM	PubChem BioAssay data set
NPT404	Cell line	CCRF-CEM	Homo sapiens	GI50	n.a.	48194.78	nM	PubChem BioAssay data set
NPT405	Cell line	NCI-H226	Homo sapiens	GI50	n.a.	34434.99	nM	PubChem BioAssay data set
NPT139	Cell line	HT-29	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT170	Cell line	SK-MEL-28	Homo sapiens	GI50	n.a.	98174.79	nM	PubChem BioAssay data set
NPT406	Cell line	RXF 393	Homo sapiens	GI50	n.a.	54450.27	nM	PubChem BioAssay data set
NPT407	Cell line	COLO 205	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set

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 NPC211386 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	24517
0.1-0.2	22904
0.2-0.3	2081
0.3-0.4	255
0.4-0.5	48
0.5-0.6	16
0.6-0.7	16
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9048	High Similarity	NPC223807
0.8571	High Similarity	NPC72796
0.8163	Intermediate Similarity	NPC176586
0.8163	Intermediate Similarity	NPC210354
0.7755	Intermediate Similarity	NPC205915
0.7647	Intermediate Similarity	NPC191158
0.7647	Intermediate Similarity	NPC177644
0.7347	Intermediate Similarity	NPC40237
0.717	Intermediate Similarity	NPC5310
0.717	Intermediate Similarity	NPC106920
0.717	Intermediate Similarity	NPC300776
0.717	Intermediate Similarity	NPC15811
0.717	Intermediate Similarity	NPC176814
0.717	Intermediate Similarity	NPC4982
0.717	Intermediate Similarity	NPC606629
0.7143	Intermediate Similarity	NPC92693
0.6939	Remote Similarity	NPC110958
0.6939	Remote Similarity	NPC19890
0.65	Remote Similarity	NPC478705
0.6491	Remote Similarity	NPC145569
0.6346	Remote Similarity	NPC143895
0.6222	Remote Similarity	NPC81067
0.6222	Remote Similarity	NPC602945
0.6167	Remote Similarity	NPC216223
0.614	Remote Similarity	NPC293757
0.614	Remote Similarity	NPC668
0.6129	Remote Similarity	NPC478703
0.6129	Remote Similarity	NPC478704
0.6038	Remote Similarity	NPC68779
0.6038	Remote Similarity	NPC108598
0.6	Remote Similarity	NPC282291
0.6	Remote Similarity	NPC166137
0.5938	Remote Similarity	NPC158635
0.5938	Remote Similarity	NPC229882
0.5893	Remote Similarity	NPC273657
0.587	Remote Similarity	NPC477886
0.566	Remote Similarity	NPC192255
0.5645	Remote Similarity	NPC174512
0.5574	Remote Similarity	NPC56184
0.537	Remote Similarity	NPC474288
0.5283	Remote Similarity	NPC11453
0.5192	Remote Similarity	NPC476748
0.5185	Remote Similarity	NPC482890
0.5091	Remote Similarity	NPC143092
0.5068	Remote Similarity	NPC299706
0.5068	Remote Similarity	NPC245615
0.5068	Remote Similarity	NPC115466
0.5068	Remote Similarity	NPC61604

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC211386 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4152
0.1-0.2	4721
0.2-0.3	257
0.3-0.4	19
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