NPASS Compound

Natural Product: NPC162925

Natural Product ID	NPC162925
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ipomotaoside A
IUPAC Name	n.a.
Synonyms	Ipomotaoside A
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1631409
PubChem CID	50900934
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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0 72180 1 0 73181 1 0 73182 1 0 74183 1 0 74184 1 0 75185 1 0 75186 1 0 76187 1 1 77188 1 0 77189 1 0 78190 1 0 78191 1 0 79192 1 0 79193 1 0 80194 1 0 80195 1 0 81196 1 0 81197 1 0 81198 1 0 83199 1 1 84200 1 6 85201 1 1 86202 1 1 87203 1 1 88204 1 0 88205 1 0 88206 1 0 90207 1 0 91208 1 0 M END

Standard InCHIKey	RWELBFDBNJXLOK-RQSNGXSLSA-N
Standard InCHI	InChI=1S/C71H116O21/c1-8-11-14-16-18-19-23-27-34-41-52(72)86-61-47(5)83-70(66(58(61)78)89-55(75)45-44-50-37-31-29-32-38-50)91-63-49(7)82-68(60(80)64(63)87-53(73)42-35-26-21-17-15-12-9-2)90-62-48(6)84-71-67(59(62)79)88-54(74)43-36-28-24-20-22-25-33-40-51(39-30-13-10-3)85-69-65(92-71)57(77)56(76)46(4)81-69/h29,31-32,37-38,44-49,51,56-71,76-80H,8-28,30,33-36,39-43H2,1-7H3/b45-44+/t46-,47+,48+,49+,51+,56+,57+,58-,59-,60-,61+,62+,63+,64+,65-,66-,67-,68+,69+,70+,71+/m1/s1
SMILES	CCCCCCCCCCCC(=O)O[C@H]1[C@H](C)O[C@H]([C@@H]([C@@H]1O)OC(=O)/C=C/c1ccccc1)O[C@H]1[C@H](C)O[C@H]([C@@H]([C@@H]1OC(=O)CCCCCCCCC)O)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCC[C@H](CCCCC)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](C)O1)O)O)O2

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1304.8	Volume:	1348.736 ? Van der Waals volume.
Dense:	0.967	LogP:	10.417 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	6.983 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.428 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	34.0	Rigid Bonds:	51.0
TPSA:	280.19 ? Topological Polar Surface Area.	H-Bond Acceptor:	21.0
H-Bond Donor:	5.0	Rings:	6.0
Heavy Atoms:	21.0

MedChem Properties

QED Drug-Likeness Score:	0.02	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.232	Fsp³:	0.831
MCE-18:	152.308 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	1.0	Fluc inhibitor:	0.666 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.152 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.306 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.331	Promiscuous compounds:	0.037

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.525	MDCK Permeability:	-4.886
Pgp-inhibitor:	0.038	Pgp-substrate:	0.364
PAMPA:	0.022 ? 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%):	0.091	30% Bioavailability (F30%):	0.906
50% Bioavailability (F50%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.997
Plasma Protein Binding (PPB):	98.704%	Volume Distribution (VD):	0.764
Fu:	1.022% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.939
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.349
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.111
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.971 ? 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):

1.637

Half-life (T1/2):

4.649

ADMET: Toxicity

hERG Blockers:	0.384	hERG Blockers (10um):	0.656
Human Hepatotoxicity (H-HT):	0.531	Drug-induced Liver Injury (DILI):	0.994
AMES Toxicity:	0.172	Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.013	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.005	Respiratory Toxicity:	0.01
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.994
Hematotoxicity:	0.397	Drug-induced Nephrotoxicity:	0.969
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.525
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.762
BCF:	1.001 ? 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:	5.926 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	7.14 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.671 ? 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
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[20961090]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24074359]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	leaf	n.a.	PMID[27132824]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	Tubers	n.a.		Database[FooDB]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2848	Ipomoea batatas	Species	Convolvulaceae	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
Individual protein	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT324	Individual protein	Cyclooxygenase-1	Ovis aries	IC50	=	9300.0	nM	PMID[20961090]
NPT325	Individual protein	Cyclooxygenase-2	Ovis aries	IC50	=	14500.0	nM	PMID[20961090]

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 NPC162925 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	14943
0.1-0.2	32017
0.2-0.3	2627
0.3-0.4	138
0.4-0.5	73
0.5-0.6	41
0.6-0.7	9
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.859	High Similarity	NPC87153
0.7604	Intermediate Similarity	NPC10121
0.7604	Intermediate Similarity	NPC198918
0.7474	Intermediate Similarity	NPC28069
0.7474	Intermediate Similarity	NPC77651
0.7245	Intermediate Similarity	NPC10883
0.7071	Intermediate Similarity	NPC290276
0.6907	Remote Similarity	NPC124878
0.6907	Remote Similarity	NPC231888
0.6881	Remote Similarity	NPC147032
0.6837	Remote Similarity	NPC35338
0.6837	Remote Similarity	NPC204214
0.6837	Remote Similarity	NPC63404
0.6837	Remote Similarity	NPC92283
0.6602	Remote Similarity	NPC471025
0.6239	Remote Similarity	NPC471024
0.5766	Remote Similarity	NPC471026
0.5667	Remote Similarity	NPC146380
0.5612	Remote Similarity	NPC483170
0.5604	Remote Similarity	NPC477330
0.5591	Remote Similarity	NPC113745
0.5591	Remote Similarity	NPC477320
0.5591	Remote Similarity	NPC477323
0.5591	Remote Similarity	NPC477325
0.5591	Remote Similarity	NPC609436
0.5543	Remote Similarity	NPC477329
0.5521	Remote Similarity	NPC109887
0.5506	Remote Similarity	NPC478729
0.5506	Remote Similarity	NPC606819
0.5481	Remote Similarity	NPC140561
0.5474	Remote Similarity	NPC89843
0.5435	Remote Similarity	NPC477328
0.5417	Remote Similarity	NPC477326
0.5408	Remote Similarity	NPC477319
0.5368	Remote Similarity	NPC604005
0.5368	Remote Similarity	NPC605014
0.5354	Remote Similarity	NPC143421
0.5354	Remote Similarity	NPC307400
0.5354	Remote Similarity	NPC27289
0.5354	Remote Similarity	NPC119583
0.5327	Remote Similarity	NPC141970
0.5327	Remote Similarity	NPC226101
0.5312	Remote Similarity	NPC477331
0.5306	Remote Similarity	NPC479061
0.5306	Remote Similarity	NPC267592
0.5278	Remote Similarity	NPC231627
0.5253	Remote Similarity	NPC479060
0.5248	Remote Similarity	NPC169345
0.5248	Remote Similarity	NPC290012
0.5248	Remote Similarity	NPC115013
0.5229	Remote Similarity	NPC237182
0.52	Remote Similarity	NPC472204
0.5196	Remote Similarity	NPC183888
0.5196	Remote Similarity	NPC224953
0.5196	Remote Similarity	NPC126685
0.5155	Remote Similarity	NPC477332
0.5146	Remote Similarity	NPC123204

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162925 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4732
0.1-0.2	4327
0.2-0.3	90
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