NPASS Compound

Natural Product: NPC209389

Natural Product ID	NPC209389
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Indigo
IUPAC Name	(2E)-2-(3-oxo-1H-indol-2-ylidene)-1H-indol-3-one
Synonyms	Indigo
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL599552
PubChem CID	5318432
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0001146] Indolines

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 30 33 0 0 0 0 0 0 0 0999 V2000 0.8785 1.2035 2.1555 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3827 0.6861 1.1337 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7937 0.5614 0.7826 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9500 0.9516 1.4286 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2126 0.7374 0.9200 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3113 0.0990 -0.2985 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1588 -0.2958 -0.9536 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8949 -0.0764 -0.4350 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5788 -0.3929 -0.9283 N 0 0 0 0 0 0 0 0 0 0 0 0 0.6402 0.0761 0.0373 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6697 -0.0638 -0.1217 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6032 0.4029 0.8389 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9003 0.0786 0.3293 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7975 -0.5578 -0.8857 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3773 -0.6785 -1.2298 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8947 -1.1996 -2.2571 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9576 -0.9595 -1.5533 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1966 -0.7351 -1.0273 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3172 -0.1010 0.1848 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1840 0.3003 0.8538 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9144 1.4643 2.4036 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1087 1.0499 1.4398 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2882 -0.0906 -0.7373 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2606 -0.7964 -1.9109 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3775 -0.8757 -1.8273 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3991 0.8871 1.7405 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7885 -1.4558 -2.5081 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0716 -1.0756 -1.6018 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3164 0.0628 0.5765 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2771 0.7936 1.7967 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 14 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 10 2 1 0 15 11 1 0 8 3 1 0 20 13 1 0 4 21 1 0 5 22 1 0 6 23 1 0 7 24 1 0 9 25 1 0 12 26 1 0 17 27 1 0 18 28 1 0 19 29 1 0 20 30 1 0 M END

Standard InCHIKey	COHYTHOBJLSHDF-BUHFOSPRSA-N
Standard InCHI	InChI=1S/C16H10N2O2/c19-15-9-5-1-3-7-11(9)17-13(15)14-16(20)10-6-2-4-8-12(10)18-14/h1-8,17-18H/b14-13+
SMILES	O=C1c2ccccc2N/C/1=C1/Nc2c(C1=O)cccc2

Calculated Properties

Physi-Chem Properties

Molecular Weight:	262.07	Volume:	266.912 ? Van der Waals volume.
Dense:	0.982	LogP:	3.058 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.813 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.059 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	23.0
TPSA:	58.2 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.717	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.341	Fsp³:	0.0
MCE-18:	40.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	1
Colloidal aggregators:	0.777	Fluc inhibitor:	0.607 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.7 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.413 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.242	Promiscuous compounds:	0.759

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.462	MDCK Permeability:	-4.615
Pgp-inhibitor:	0.999	Pgp-substrate:	0.0
PAMPA:	0.128 ? 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):	0.881
20% Bioavailability (F20%):	0.002	30% Bioavailability (F30%):	0.947
50% Bioavailability (F50%):	0.502

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.001
Plasma Protein Binding (PPB):	96.226%	Volume Distribution (VD):	0.278
Fu:	4.104% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.98

ADMET: Metabolism

CYP1A2-inhibitor:	0.999	CYP1A2-substrate:	0.303
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.841
CYP3A4-inhibitor:	0.011	CYP3A4-substrate:	0.874
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.834 ? 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):

5.069

Half-life (T1/2):

0.835

ADMET: Toxicity

hERG Blockers:	0.162	hERG Blockers (10um):	0.473
Human Hepatotoxicity (H-HT):	0.773	Drug-induced Liver Injury (DILI):	0.962
AMES Toxicity:	0.417	Rat Oral Acute Toxicity:	0.529
Maximum Recommended Daily Dose:	0.409	Skin Sensitization:	0.412
Carcinogencity:	0.16	Eye Corrosion:	0.001
Eye Irritation:	0.862	Respiratory Toxicity:	0.41
Drug-induced Neurotoxicity:	0.57	Ototoxicity:	0.408
Hematotoxicity:	0.356	Drug-induced Nephrotoxicity:	0.609
Genotoxicity:	0.984	RPMI-8226 Immunitoxicity:	0.023
A549 Cytotoxicity:	0.072	Hek293 Cytotoxicity:	0.189
BCF:	1.497 ? 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:	4.424 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.507 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.37 ? 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
NPO31573	Polygonum tinctorium	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11678654]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787451]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	Roots	Anhui, China	n.a.	PMID[22694318]
NPO8274	Geijera parviflora	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23848189]
NPO6485	Spiraea japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24684844]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	Cupules	n.a.	n.a.	PMID[25098388]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[26434122]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32004936]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39053741]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8274	Geijera parviflora	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6485	Spiraea japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31573	Polygonum tinctorium	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9069	Persicaria tinctoria	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15694	Corydalis cheilanthifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31573	Polygonum tinctorium	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6485	Spiraea japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1007	Crotalaria paniculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6485	Spiraea japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15694	Corydalis cheilanthifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9069	Persicaria tinctoria	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30657	Lndigofera tinctoria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31573	Polygonum tinctorium	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31050	Isatis indigotica	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9069	Persicaria tinctoria	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15101	Tricholoma panaeolum	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8274	Geijera parviflora	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26308	Lithocarpus polystachyus	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15694	Corydalis cheilanthifolia	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6485	Spiraea japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9069	Persicaria tinctoria	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12718	Simira salvadorensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4520	Allium macrostemon	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1007	Crotalaria paniculata	Species	Fabaceae	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
Potency	22
IC50	10
Change in IC50	2
EC50	2
MIC	1
AC50	3

Activity Type	# Activity
Individual protein	18
Protein complex	3
Organism	2
Protein family	1
Others	16

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT152	Individual protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	18832.2	nM	PubChem BioAssay data set
NPT1371	Individual protein	Cyclin-dependent kinase 2	Homo sapiens	IC50	=	70000.0	nM	PMID[12672248]
NPT1564	Individual protein	Malate dehydrogenase	Thermus thermophilus	IC50	=	60000.0	nM	PMID[12672248]
NPT155	Individual protein	Aryl hydrocarbon receptor	Homo sapiens	EC50	=	1700.0	nM	PMID[20060304]
NPT155	Individual protein	Aryl hydrocarbon receptor	Homo sapiens	EC50	=	5.0	nM	PMID[36274276]
NPT1509	Protein complex	Cyclin-dependent kinase 5/CDK5 activator 1	Homo sapiens	IC50	>	100000.0	nM	PMID[15163202]
NPT607	Individual protein	Beta-chymotrypsin	Homo sapiens	IC50	=	90000.0	nM	PMID[12672248]
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	=	3548.1	nM	PubChem BioAssay data set
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	39810.7	nM	PubChem BioAssay data set
NPT36	Individual protein	Tyrosine-protein kinase SRC	Homo sapiens	IC50	=	28000.0	nM	PMID[12672248]
NPT94	Individual protein	Aldehyde dehydrogenase 1A1	Homo sapiens	Potency	=	3162.3	nM	PubChem BioAssay data set
NPT444	Individual protein	Ubiquitin carboxyl-terminal hydrolase 1	Homo sapiens	Potency	n.a.	63095.7	nM	PubChem BioAssay data set
NPT484	Individual protein	Luciferin 4-monooxygenase	Photinus pyralis	Potency	n.a.	12817.8	nM	PubChem BioAssay data set
NPT583	Individual protein	Inositol monophosphatase 1	Rattus norvegicus	Potency	=	3162.3	nM	PubChem BioAssay data set
NPT1570	Protein complex	Cyclin-dependent kinase 1/cyclin B	Homo sapiens	IC50	>	100000.0	nM	PMID[15163202]
NPT1572	Protein family	Glycogen synthase kinase-3	Homo sapiens	IC50	>	100000.0	nM	PMID[15163202]
NPT56	Individual protein	Beta-lactamase AmpC	Escherichia coli K-12	Change in IC50	>	50.0	fold	PMID[12672248]
NPT62	Individual protein	6-phospho-1-fructokinase	Trypanosoma brucei	Potency	n.a.	7943.3	nM	PubChem BioAssay data set
NPT5	Individual protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency	n.a.	5011.9	nM	PubChem BioAssay data set
NPT49	Individual protein	DNA-(apurinic or apyrimidinic site) lyase	Homo sapiens	Potency	n.a.	7943.3	nM	PubChem BioAssay data set
NPT3944	Protein complex	Cyclin-dependent kinase 2/cyclin E1	Homo sapiens	IC50	=	1000.0	nM	PMID[26706352]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	9528.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	4216.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	1216	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	11883.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	943.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	60944.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	1083.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	26603.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	33491.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	7497.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	IC50	=	200000.0	nM	DOI[10.1016/S0960-894X(00)80378-9]
NPT2	Others	Unspecified	n.a.	IC50	=	30000.0	nM	PMID[12672248]
NPT790	Organism	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis H37Rv	MIC	>	32000.0	nM	PMID[24314672]
NPT2	Others	Unspecified	n.a.	Potency	n.a.	22387.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	AC50	n.a.	15848.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	AC50	n.a.	25118.9	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 NPC209389 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	34834
0.1-0.2	14480
0.2-0.3	513
0.3-0.4	24
0.4-0.5	6
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	Natural Product ID
		NPC

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC209389 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4730
0.1-0.2	4233
0.2-0.3	185
0.3-0.4	1
0.4-0.5	0
0.5-0.6	1
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
0.5122	Remote Similarity	NPD1854	Phase 4

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