NPASS Compound

Natural Product: NPC87153

Natural Product ID	NPC87153
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ipomotaoside B
IUPAC Name	n.a.
Synonyms	Ipomotaoside B
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1631410
PubChem CID	50901029
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 52154 1 0 52155 1 0 53156 1 0 53157 1 0 54158 1 0 54159 1 0 55160 1 0 55161 1 0 55162 1 0 56163 1 0 56164 1 0 56165 1 0 58166 1 1 59167 1 6 60168 1 0 60169 1 0 60170 1 0 62171 1 1 63172 1 6 64173 1 6 65174 1 0 69175 1 0 69176 1 0 70177 1 0 70178 1 0 71179 1 0 71180 1 0 72181 1 0 72182 1 0 73183 1 0 73184 1 0 74185 1 0 74186 1 0 75187 1 0 75188 1 0 76189 1 0 76190 1 0 77191 1 0 77192 1 0 78193 1 1 80194 1 1 81195 1 6 83196 1 1 84197 1 0 85198 1 1 86199 1 1 88200 1 0 88201 1 0 88202 1 0 89203 1 0 90204 1 0 90205 1 0 91206 1 0 91207 1 0 92208 1 0 92209 1 0 93210 1 0 93211 1 0 94212 1 0 94213 1 0 94214 1 0 M END

Standard InCHIKey	FSDJTONUQZBFFY-QSAXEEFWSA-N
Standard InCHI	InChI=1S/C73H120O21/c1-8-11-14-16-18-20-24-28-36-43-54(74)88-63-49(5)84-71(67(60(63)80)91-57(77)47-46-52-39-33-31-34-40-52)92-64-50(6)85-72(68(61(64)81)89-55(75)44-37-29-25-21-19-17-15-12-9-2)93-65-51(7)86-73-69(62(65)82)90-56(76)45-38-30-26-22-23-27-35-42-53(41-32-13-10-3)87-70-66(94-73)59(79)58(78)48(4)83-70/h31,33-34,39-40,46-51,53,58-73,78-82H,8-30,32,35-38,41-45H2,1-7H3/b47-46+/t48-,49+,50+,51+,53+,58+,59+,60-,61-,62-,63+,64+,65+,66-,67-,68-,69-,70+,71+,72+,73+/m1/s1
SMILES	CCCCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)/C=C/c1ccccc1)O)OC(=O)CCCCCCCCCCC)C)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCC[C@@H](O[C@H]1[C@H](O2)[C@@H](O)[C@H]([C@H](O1)C)O)CCCCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1332.83	Volume:	1383.328 ? Van der Waals volume.
Dense:	0.963	LogP:	11.608 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	7.277 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.715 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	36.0	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:	0.019	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.25	Fsp³:	0.836
MCE-18:	151.701 ? 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:	0.665 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.121 ? 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:	0.355	Promiscuous compounds:	0.038

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.552	MDCK Permeability:	-4.765
Pgp-inhibitor:	0.011	Pgp-substrate:	0.325
PAMPA:	0.011 ? 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):	0.005
20% Bioavailability (F20%):	0.108	30% Bioavailability (F30%):	0.949
50% Bioavailability (F50%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.996
Plasma Protein Binding (PPB):	98.96%	Volume Distribution (VD):	0.869
Fu:	0.896% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.98
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.873
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.007
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.93 ? 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):

1.76

Half-life (T1/2):

5.127

ADMET: Toxicity

hERG Blockers:	0.518	hERG Blockers (10um):	0.712
Human Hepatotoxicity (H-HT):	0.604	Drug-induced Liver Injury (DILI):	0.995
AMES Toxicity:	0.132	Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.016	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.007	Respiratory Toxicity:	0.022
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.993
Hematotoxicity:	0.416	Drug-induced Nephrotoxicity:	0.968
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.553
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.839
BCF:	0.901 ? 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:	6.112 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	7.306 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.6 ? 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	=	132000.0	nM	PMID[20961090]
NPT325	Individual protein	Cyclooxygenase-2	Ovis aries	IC50	=	147000.0	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 NPC87153 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	11041
0.1-0.2	35021
0.2-0.3	3428
0.3-0.4	227
0.4-0.5	97
0.5-0.6	28
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	NPC162925
0.764	Intermediate Similarity	NPC28069
0.7204	Intermediate Similarity	NPC290276
0.7065	Intermediate Similarity	NPC77651
0.6842	Remote Similarity	NPC10883
0.6667	Remote Similarity	NPC10121
0.6667	Remote Similarity	NPC198918
0.6355	Remote Similarity	NPC147032
0.622	Remote Similarity	NPC477330
0.62	Remote Similarity	NPC471025
0.6145	Remote Similarity	NPC477329
0.6125	Remote Similarity	NPC478729
0.6024	Remote Similarity	NPC477328
0.5979	Remote Similarity	NPC124878
0.5979	Remote Similarity	NPC231888
0.5918	Remote Similarity	NPC35338
0.5918	Remote Similarity	NPC204214
0.5918	Remote Similarity	NPC63404
0.5918	Remote Similarity	NPC92283
0.5862	Remote Similarity	NPC477331
0.5849	Remote Similarity	NPC471024
0.581	Remote Similarity	NPC471026
0.5682	Remote Similarity	NPC89843
0.5682	Remote Similarity	NPC477332
0.5556	Remote Similarity	NPC109887
0.5405	Remote Similarity	NPC206823
0.5376	Remote Similarity	NPC119583
0.5326	Remote Similarity	NPC479061
0.5269	Remote Similarity	NPC479060
0.5263	Remote Similarity	NPC169345
0.5263	Remote Similarity	NPC115013
0.5208	Remote Similarity	NPC224953
0.52	Remote Similarity	NPC140561
0.5176	Remote Similarity	NPC606819
0.5161	Remote Similarity	NPC60849
0.5158	Remote Similarity	NPC483170
0.5152	Remote Similarity	NPC478727
0.5052	Remote Similarity	NPC479057
0.5051	Remote Similarity	NPC478728
0.5049	Remote Similarity	NPC141970
0.5049	Remote Similarity	NPC226101

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC87153 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3999
0.1-0.2	4988
0.2-0.3	163
0.3-0.4	0
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