NPASS Compound

Natural Product: NPC154275

Natural Product ID	NPC154275
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Veratric Acid Methyl Ester
IUPAC Name	methyl 3,4-dimethoxybenzoate
Synonyms	Methyl 3,4-Dimethoxybenzoate
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL446736
PubChem CID	16522
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0002344] Methoxybenzoic acids and derivatives [CHEMONTID:0002346] P-methoxybenzoic 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 26 26 0 0 0 0 0 0 0 0999 V2000 -3.6271 2.2684 0.7039 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0218 1.0139 0.6041 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6742 0.8060 0.4157 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8201 1.8857 0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5174 1.6776 0.1251 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0351 0.4091 0.0372 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1566 -0.6625 0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1845 -0.4671 0.3315 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0348 -1.5396 0.4346 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6079 -2.8831 0.3582 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4599 0.2509 -0.1612 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1908 1.2635 -0.2487 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0866 -0.9833 -0.2637 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4662 -1.1501 -0.4560 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6802 2.0994 1.0638 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1240 2.9416 1.4245 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6794 2.7501 -0.2978 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2216 2.8841 0.3805 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1632 2.5665 0.0478 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6157 -1.6471 0.0680 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5513 -3.1657 -0.7293 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4053 -3.5326 0.7823 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6381 -3.0588 0.8404 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7106 -2.2172 -0.2110 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7755 -0.9807 -1.5078 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0926 -0.5291 0.2059 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 2 0 8 9 1 0 9 10 1 0 6 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 8 3 1 0 1 15 1 0 1 16 1 0 1 17 1 0 4 18 1 0 5 19 1 0 7 20 1 0 10 21 1 0 10 22 1 0 10 23 1 0 14 24 1 0 14 25 1 0 14 26 1 0 M END

Standard InCHIKey	BIGQPYZPEWAPBG-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H12O4/c1-12-8-5-4-7(10(11)14-3)6-9(8)13-2/h4-6H,1-3H3
SMILES	COc1ccc(cc1OC)C(=O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	196.07	Volume:	197.575 ? Van der Waals volume.
Dense:	0.992	LogP:	2.038 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.244 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.735 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	7.0
TPSA:	44.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.687	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.376	Fsp³:	0.3
MCE-18:	7.0 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.039	Fluc inhibitor:	0.009 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.027 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.1 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.982	Promiscuous compounds:	0.375

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.556	MDCK Permeability:	-4.558
Pgp-inhibitor:	0.884	Pgp-substrate:	0.089
PAMPA:	0.02 ? 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):	0.022
20% Bioavailability (F20%):	0.206	30% Bioavailability (F30%):	0.147
50% Bioavailability (F50%):	0.855

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.071	MRP1:	0.994
Plasma Protein Binding (PPB):	90.822%	Volume Distribution (VD):	0.123
Fu:	8.942% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.917
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.927
BSEP inhibitor:	0.968

ADMET: Metabolism

CYP1A2-inhibitor:	0.992	CYP1A2-substrate:	0.878
CYP2C19-inhibitor:	0.995	CYP2C19-substrate:	0.435
CYP2C9-inhibitor:	0.982	CYP2C9-substrate:	0.059
CYP2D6-inhibitor:	0.998	CYP2D6-substrate:	0.824
CYP3A4-inhibitor:	0.828	CYP3A4-substrate:	0.154
CYP2B6-substrate:	0.431	CYP2C8-inhibitor:	0.971
HLM stability:	0.996 ? 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):

7.037

Half-life (T1/2):

1.794

ADMET: Toxicity

hERG Blockers:	0.101	hERG Blockers (10um):	0.557
Human Hepatotoxicity (H-HT):	0.197	Drug-induced Liver Injury (DILI):	0.518
AMES Toxicity:	0.4	Rat Oral Acute Toxicity:	0.25
Maximum Recommended Daily Dose:	0.191	Skin Sensitization:	0.444
Carcinogencity:	0.688	Eye Corrosion:	0.745
Eye Irritation:	0.989	Respiratory Toxicity:	0.446
Drug-induced Neurotoxicity:	0.545	Ototoxicity:	0.176
Hematotoxicity:	0.155	Drug-induced Nephrotoxicity:	0.172
Genotoxicity:	0.05	RPMI-8226 Immunitoxicity:	0.059
A549 Cytotoxicity:	0.036	Hek293 Cytotoxicity:	0.148
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:	3.248 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.01 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.697 ? 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
NPO23276	Flavoparmelia euplecta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10650094]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan soft coral	n.a.	PMID[11141107]
NPO23405	Sidnyum turbinatum	n.a.	n.a.	n.a.	n.a.	Mediterranean	n.a.	PMID[11430005]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575955]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan soft coral	n.a.	PMID[12398540]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[15104486]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	stems	Yunnan Province, China	2004	PMID[17253844]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	Stems	purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea	2006-APR	PMID[18052323]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	tubers	n.a.	n.a.	PMID[18348533]
NPO2188	Dendrobium candidum	Species	Orchidaceae	Eukaryota	n.a.	stem	n.a.	PMID[19182417]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19572610]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20209910]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	n.a.	tuber	n.a.	PMID[21322946]
NPO14429	Nocardiopsis dassonvillei	Species	Nocardiopsaceae	Bacteria	n.a.	spore	n.a.	PMID[21958359]
NPO14429	Nocardiopsis dassonvillei	Species	Nocardiopsaceae	Bacteria	isolated from marine sediments	The estuary of Yellow River, Dongying, Shandong Province, China	n.a.	PMID[21958359]
NPO23332	Dendrobium fimbriatum	Species	Orchidaceae	Eukaryota	stems	n.a.	n.a.	PMID[25316316]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26035239]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	Stems	n.a.	n.a.	PMID[27310249]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	n.a.	n.a.	PMID[30994348]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36985838]
NPO16849	Melaleuca linariifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2188	Dendrobium candidum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23332	Dendrobium fimbriatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17075	Relicina sydneyensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15365	Maytenus heterophylla	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13979	Tilia argentea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14429	Nocardiopsis dassonvillei	Species	Nocardiopsaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11889	Dendrobium chrysanthum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23405	Sidnyum turbinatum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23951	Oxytropis muricata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23276	Flavoparmelia euplecta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4019	Anabaena laxa	Species	Nostocaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23997	Adesmia boronioides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20283	Croton ruizianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13979	Tilia argentea	Species	Malvaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15365	Maytenus heterophylla	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11889	Dendrobium chrysanthum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2188	Dendrobium candidum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23332	Dendrobium fimbriatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11889	Dendrobium chrysanthum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4335	Anthracocystis flocculosa	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18380	Marsdenia tinctoria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18525	Diosma prama	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23276	Flavoparmelia euplecta	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20283	Croton ruizianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13979	Tilia argentea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9768	Matricaria globifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3894	Dendrobium nobile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14429	Nocardiopsis dassonvillei	Species	Nocardiopsaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16130	Streptomyces longwoodensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10742	Galium verum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23997	Adesmia boronioides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12933	Gymnadenia conopsea	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17075	Relicina sydneyensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2188	Dendrobium candidum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23332	Dendrobium fimbriatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20900	Dendrobium chrysotoxum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23951	Oxytropis muricata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16849	Melaleuca linariifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11889	Dendrobium chrysanthum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4019	Anabaena laxa	Species	Nostocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19193	Chrysanthemum monspeliense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23405	Sidnyum turbinatum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO15365	Maytenus heterophylla	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	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
MIC	5
-logMIC	5
CC50	1

Activity Type	# Activity
Cell line	1
Organism	10

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
NPT616	Cell line	MDCK	Canis lupus familiaris	CC50	>	169990.0	nM	PMID[24803363]
NPT21	Organism	Aspergillus niger	Aspergillus niger	MIC	=	14.0	ug.mL-1	PMID[18597896]
NPT21	Organism	Aspergillus niger	Aspergillus niger	-logMIC	=	1.15	n.a.	PMID[18597896]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	12.0	ug.mL-1	PMID[18597896]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	-logMIC	=	1.2	n.a.	PMID[18597896]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	12.0	ug.mL-1	PMID[18597896]
NPT20	Organism	Candida albicans	Candida albicans	-logMIC	=	1.2	n.a.	PMID[18597896]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	18.0	ug.mL-1	PMID[18597896]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	-logMIC	=	1.04	n.a.	PMID[18597896]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	18.0	ug.mL-1	PMID[18597896]
NPT19	Organism	Escherichia coli	Escherichia coli	-logMIC	=	1.04	n.a.	PMID[18597896]

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 NPC154275 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	27079
0.1-0.2	19188
0.2-0.3	3237
0.3-0.4	285
0.4-0.5	53
0.5-0.6	10
0.6-0.7	3
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
0.7273	Intermediate Similarity	NPC486257
0.6786	Remote Similarity	NPC220540
0.6552	Remote Similarity	NPC299010
0.6098	Remote Similarity	NPC473090
0.561	Remote Similarity	NPC254120
0.5581	Remote Similarity	NPC473091
0.5581	Remote Similarity	NPC486252
0.5581	Remote Similarity	NPC486253
0.5581	Remote Similarity	NPC486254
0.5581	Remote Similarity	NPC486255
0.5333	Remote Similarity	NPC12714
0.5278	Remote Similarity	NPC159418
0.5185	Remote Similarity	NPC203925
0.5161	Remote Similarity	NPC295317

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC154275 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4209
0.1-0.2	4594
0.2-0.3	319
0.3-0.4	24
0.4-0.5	4
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