NPASS Compound

Natural Product: NPC140543

Natural Product ID	NPC140543
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Scandenolide
IUPAC Name	n.a.
Synonyms	Scandenolide
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL424997
PubChem CID	44398226
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids 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 42 45 0 0 0 0 0 0 0 0999 V2000 -3.9559 -2.4232 -0.3108 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5398 -1.3322 0.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1640 -0.8920 0.6423 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1581 -1.1629 -0.3489 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1252 -0.9222 0.3076 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0113 -1.0292 -0.6452 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1496 -0.1419 -0.5489 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8746 1.1046 0.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8719 2.0456 -0.2245 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4475 2.1826 0.0505 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1376 3.5024 -0.4266 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2659 1.4920 1.0677 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3610 0.6199 0.6201 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5794 0.7523 1.3141 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4020 -0.2615 0.7814 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6708 -0.2103 0.7508 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0177 1.5608 -1.1441 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1659 -0.8467 0.1862 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4259 -1.0888 -0.3291 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6535 -0.6573 -1.4956 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4680 -1.8230 0.4507 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4280 -2.0927 -1.4787 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9686 -2.5177 -2.5055 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8003 -2.4480 -0.8255 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0000 -2.6232 -0.5042 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2713 -3.2014 -0.6594 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9313 -1.2659 1.6443 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3806 -0.6062 -1.2781 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3351 -0.7326 1.3205 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6211 0.1130 -1.5219 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9056 1.5648 0.4152 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6113 0.7872 1.3135 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4081 2.9695 -0.6583 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4557 4.0711 0.4562 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0585 3.1480 -0.9347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4891 4.0325 -1.1206 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8520 2.3383 1.6092 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6987 1.1590 1.9882 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5765 0.8587 -0.4603 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0284 -1.0724 1.0273 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1575 -2.3740 -0.2114 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0042 -2.5770 1.1225 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 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 6 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 10 17 1 0 7 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 6 22 1 0 22 23 2 0 22 24 1 0 15 2 1 0 13 3 1 0 24 4 1 0 17 9 1 0 1 25 1 0 1 26 1 0 3 27 1 1 4 28 1 6 5 29 1 0 7 30 1 6 8 31 1 0 8 32 1 0 9 33 1 6 11 34 1 0 11 35 1 0 11 36 1 0 12 37 1 0 12 38 1 0 13 39 1 6 21 40 1 0 21 41 1 0 21 42 1 0 M END

Standard InCHIKey	SLIMCFUYVZKJTC-WFTXNEMLSA-N
Standard InCHI	InChI=1S/C17H18O7/c1-7-14-11-4-9(16(20)22-11)10(21-8(2)18)5-13-17(3,24-13)6-12(14)23-15(7)19/h4,10-14H,1,5-6H2,2-3H3/t10-,11-,12+,13-,14+,17+/m1/s1
SMILES	C=C1[C@H]2[C@H]3C=C([C@@H](C[C@@H]4[C@](C)(C[C@@H]2OC1=O)O4)OC(=O)C)C(=O)O3

Calculated Properties

Physi-Chem Properties

Molecular Weight:	334.11	Volume:	316.712 ? Van der Waals volume.
Dense:	1.055	LogP:	0.566 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.92 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.085 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	23.0
TPSA:	91.43 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	0.0	Rings:	4.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.303	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.898	Fsp³:	0.588
MCE-18:	64.815 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.556	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.129 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.003 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.518	Promiscuous compounds:	0.758

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.995	MDCK Permeability:	-4.569
Pgp-inhibitor:	0.192	Pgp-substrate:	0.526
PAMPA:	0.725 ? 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):	0.078
20% Bioavailability (F20%):	0.897	30% Bioavailability (F30%):	0.981
50% Bioavailability (F50%):	0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.569	MRP1:	0.968
Plasma Protein Binding (PPB):	32.757%	Volume Distribution (VD):	-0.138
Fu:	70.251% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.996
OATP1B3 inhibitor:	0.993	BCRP inhibitor:	0.023
BSEP inhibitor:	0.939

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.005
CYP2C19-inhibitor:	0.469	CYP2C19-substrate:	0.004
CYP2C9-inhibitor:	0.032	CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.005
CYP3A4-inhibitor:	0.044	CYP3A4-substrate:	0.003
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.975
HLM stability:	0.88 ? 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):

4.994

Half-life (T1/2):

2.14

ADMET: Toxicity

hERG Blockers:	0.021	hERG Blockers (10um):	0.132
Human Hepatotoxicity (H-HT):	0.68	Drug-induced Liver Injury (DILI):	0.984
AMES Toxicity:	0.872	Rat Oral Acute Toxicity:	0.346
Maximum Recommended Daily Dose:	0.519	Skin Sensitization:	0.998
Carcinogencity:	0.689	Eye Corrosion:	0.064
Eye Irritation:	0.623	Respiratory Toxicity:	0.033
Drug-induced Neurotoxicity:	0.703	Ototoxicity:	0.539
Hematotoxicity:	0.591	Drug-induced Nephrotoxicity:	0.948
Genotoxicity:	0.98	RPMI-8226 Immunitoxicity:	0.165
A549 Cytotoxicity:	0.471	Hek293 Cytotoxicity:	0.176
BCF:	0.674 ? 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:	3.354 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.819 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.461 ? 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
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	barks	n.a.	n.a.	PMID[15620248]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19267453]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20430633]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20499851]
NPO23998	Auxarthron reticulatum	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24900275]
NPO6403	Phlegmariurus squarrosus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32941036]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37635675]
NPO24662	Ulmus laevis	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20331	Aerva tomentosa	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23866	Anisocycla cymosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23134	Artemisia kaschgarica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23998	Auxarthron reticulatum	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24854	Beltrania rhombica	Species	Beltraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24142	Cereus ocamponis	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25683	Columba livia	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25241	Cordyla africana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25313	Satureja douglasii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25341	Sanango racemosum	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25115	Psychotria calocarpa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6403	Phlegmariurus squarrosus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25399	Patrinia intermedia	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24895	Parmelia springtonensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1827	Morinda elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24242	Haminoea cymbalum	Species	Haminoeidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24950	Eupatorium aschenbornianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25602	Crotalaria barbata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24950	Eupatorium aschenbornianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24142	Cereus ocamponis	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23134	Artemisia kaschgarica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23707	Sinularia gyrosa	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1827	Morinda elliptica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25341	Sanango racemosum	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25515	Garcinia speciosa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24950	Eupatorium aschenbornianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25241	Cordyla africana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23866	Anisocycla cymosa	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24242	Haminoea cymbalum	Species	Haminoeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25683	Columba livia	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6403	Phlegmariurus squarrosus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25115	Psychotria calocarpa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22408	Aconitum polyschistum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24662	Ulmus laevis	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20331	Aerva tomentosa	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23998	Auxarthron reticulatum	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24708	Mikania micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24854	Beltrania rhombica	Species	Beltraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25602	Crotalaria barbata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25399	Patrinia intermedia	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28627	Coptis trifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25313	Satureja douglasii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24895	Parmelia springtonensis	Species	Parmeliaceae	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
IC100	2
pIC100	1

Activity Type	# Activity
Protein complex	2
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT983	Protein complex	Nuclear factor NF-kappa-B complex	Homo sapiens	IC100	=	10.0	uM	PMID[15537359]
NPT983	Protein complex	Nuclear factor NF-kappa-B complex	Homo sapiens	pIC100	=	-1.0	n.a.	PMID[15537359]
NPT721	Individual protein	Nuclear factor NF-kappa-B p65 subunit	Homo sapiens	IC100	=	10.0	uM	PMID[16570920]

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 NPC140543 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	22573
0.1-0.2	24917
0.2-0.3	1931
0.3-0.4	347
0.4-0.5	78
0.5-0.6	7
0.6-0.7	4
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
0.7091	Intermediate Similarity	NPC230800
0.6792	Remote Similarity	NPC476267
0.6724	Remote Similarity	NPC96018
0.6604	Remote Similarity	NPC35498
0.6226	Remote Similarity	NPC50637
0.5893	Remote Similarity	NPC475838
0.5893	Remote Similarity	NPC488303
0.5893	Remote Similarity	NPC125674
0.5893	Remote Similarity	NPC228451
0.5484	Remote Similarity	NPC474247
0.5424	Remote Similarity	NPC484204
0.5179	Remote Similarity	NPC475087

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC140543 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7408
0.1-0.2	1722
0.2-0.3	19
0.3-0.4	1
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