NPASS Compound

Natural Product: NPC290276

Natural Product ID	NPC290276
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Purginoside I
IUPAC Name	n.a.
Synonyms	Purginoside I
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2336640
PubChem CID	53355579
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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88 1 0 88 89 1 0 88 90 1 0 87 91 1 0 80 92 1 0 92 93 1 0 93 94 1 0 94 95 1 0 95 96 1 0 18 13 1 0 27 20 1 0 38 32 1 0 49 44 1 0 66 60 1 0 89 82 1 0 84 64 1 0 1 97 1 0 1 98 1 0 1 99 1 0 2100 1 0 2101 1 0 3102 1 0 3103 1 0 4104 1 0 4105 1 0 5106 1 0 5107 1 0 6108 1 0 6109 1 0 7110 1 0 7111 1 0 8112 1 0 8113 1 0 9114 1 0 9115 1 0 13116 1 6 14117 1 1 16118 1 6 17119 1 1 18120 1 6 20121 1 6 22122 1 6 23123 1 0 23124 1 0 24125 1 0 25126 1 1 26127 1 6 27128 1 1 28129 1 0 29130 1 0 30131 1 0 32132 1 6 34133 1 1 35134 1 0 35135 1 0 35136 1 0 36137 1 6 37138 1 1 38139 1 1 42140 1 0 43141 1 0 45142 1 0 46143 1 0 47144 1 0 48145 1 0 49146 1 0 50147 1 0 54148 1 1 55149 1 0 55150 1 0 56151 1 0 56152 1 0 56153 1 0 57154 1 0 57155 1 0 57156 1 0 58157 1 0 58158 1 0 58159 1 0 60160 1 1 61161 1 6 62162 1 0 62163 1 0 62164 1 0 64165 1 1 65166 1 6 66167 1 6 67168 1 0 71169 1 0 71170 1 0 72171 1 0 72172 1 0 73173 1 0 73174 1 0 74175 1 0 74176 1 0 75177 1 0 75178 1 0 76179 1 0 76180 1 0 77181 1 0 77182 1 0 78183 1 0 78184 1 0 79185 1 0 79186 1 0 80187 1 1 82188 1 1 83189 1 6 85190 1 1 86191 1 0 87192 1 1 88193 1 1 90194 1 0 90195 1 0 90196 1 0 91197 1 0 92198 1 0 92199 1 0 93200 1 0 93201 1 0 94202 1 0 94203 1 0 95204 1 0 95205 1 0 96206 1 0 96207 1 0 96208 1 0 M END

Standard InCHIKey	MFVVQPJPHUAJBA-KXXSYOAGSA-N
Standard InCHI	InChI=1S/C70H112O26/c1-9-12-14-15-17-21-29-35-48(73)91-64-63(96-66-54(79)52(77)51(76)46(38-71)88-66)59(94-68-61(90-49(74)37-36-44-30-25-23-26-31-44)55(80)57(41(6)84-68)92-65(82)39(4)11-3)43(8)86-70(64)93-58-42(7)85-69-62(56(58)81)89-47(72)34-28-22-19-16-18-20-27-33-45(32-24-13-10-2)87-67-60(95-69)53(78)50(75)40(5)83-67/h23,25-26,30-31,36-37,39-43,45-46,50-64,66-71,75-81H,9-22,24,27-29,32-35,38H2,1-8H3/b37-36+/t39-,40+,41-,42-,43-,45-,46+,50-,51+,52-,53-,54+,55+,56+,57-,58-,59-,60+,61+,62+,63+,64+,66-,67-,68-,69-,70-/m0/s1
SMILES	CCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)/C=C/c1ccccc1)O)OC(=O)[C@H](CC)C)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:	1368.74	Volume:	1366.834 ? Van der Waals volume.
Dense:	1.001	LogP:	5.586 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.877 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.154 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	29.0	Rigid Bonds:	57.0
TPSA:	359.34 ? Topological Polar Surface Area.	H-Bond Acceptor:	26.0
H-Bond Donor:	8.0	Rings:	7.0
Heavy Atoms:	26.0

MedChem Properties

QED Drug-Likeness Score:	0.024	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.663	Fsp³:	0.829
MCE-18:	187.984 ? 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:	0.208 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.312 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.406	Promiscuous compounds:	0.042

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.558	MDCK Permeability:	-5.02
Pgp-inhibitor:	0.001	Pgp-substrate:	0.484
PAMPA:	0.98 ? 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):	0.001
20% Bioavailability (F20%):	0.002	30% Bioavailability (F30%):	0.856
50% Bioavailability (F50%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.843
Plasma Protein Binding (PPB):	95.773%	Volume Distribution (VD):	-0.259
Fu:	3.71% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.46

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.795 ? 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):

0.56

Half-life (T1/2):

3.563

ADMET: Toxicity

hERG Blockers:	0.043	hERG Blockers (10um):	0.1
Human Hepatotoxicity (H-HT):	0.645	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.66	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.001	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.999
Hematotoxicity:	0.719	Drug-induced Nephrotoxicity:	0.99
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.67
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.742
BCF:	0.501 ? 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:	4.46 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.185 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.978 ? 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
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21446661]
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23273047]
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19106	Ipomoea purga	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
FC	3
IC50	2

Activity Type	# Activity
Cell line	3
Individual protein	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FC	=	2.9	n.a.	PMID[23273047]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FC	=	2.8	n.a.	PMID[23273047]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	25.0	ug.mL-1	PMID[23273047]
NPT83	Cell line	MCF7	Homo sapiens	FC	=	0.8	n.a.	PMID[23273047]

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 NPC290276 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	13719
0.1-0.2	31047
0.2-0.3	4615
0.3-0.4	343
0.4-0.5	29
0.5-0.6	45
0.6-0.7	38
0.7-0.8	0
0.8-0.85	4
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9053	High Similarity	NPC28069
0.8598	High Similarity	NPC147032
0.8469	Intermediate Similarity	NPC77651
0.8218	Intermediate Similarity	NPC10121
0.8218	Intermediate Similarity	NPC198918
0.8218	Intermediate Similarity	NPC10883
0.7778	Intermediate Similarity	NPC471024
0.7526	Intermediate Similarity	NPC224953
0.7383	Intermediate Similarity	NPC471025
0.7308	Intermediate Similarity	NPC35338
0.7308	Intermediate Similarity	NPC204214
0.7308	Intermediate Similarity	NPC92283
0.7273	Intermediate Similarity	NPC471026
0.7234	Intermediate Similarity	NPC477331
0.7204	Intermediate Similarity	NPC87153
0.7143	Intermediate Similarity	NPC63404
0.7071	Intermediate Similarity	NPC162925
0.7053	Intermediate Similarity	NPC89843
0.7	Intermediate Similarity	NPC184915
0.697	Remote Similarity	NPC483170
0.6907	Remote Similarity	NPC109887
0.6887	Remote Similarity	NPC124878
0.6887	Remote Similarity	NPC231888
0.6869	Remote Similarity	NPC119583
0.6863	Remote Similarity	NPC44782
0.6733	Remote Similarity	NPC169345
0.6733	Remote Similarity	NPC115013
0.6667	Remote Similarity	NPC183888
0.6602	Remote Similarity	NPC472200
0.6531	Remote Similarity	NPC477332
0.6505	Remote Similarity	NPC126685
0.6495	Remote Similarity	NPC22742
0.6495	Remote Similarity	NPC477346
0.6471	Remote Similarity	NPC478726
0.6465	Remote Similarity	NPC477344
0.6452	Remote Similarity	NPC478729
0.6415	Remote Similarity	NPC478727
0.6373	Remote Similarity	NPC472204
0.6364	Remote Similarity	NPC478734
0.6354	Remote Similarity	NPC477328
0.6354	Remote Similarity	NPC477330
0.6321	Remote Similarity	NPC478728
0.6289	Remote Similarity	NPC477329
0.6238	Remote Similarity	NPC478733
0.619	Remote Similarity	NPC259294
0.6176	Remote Similarity	NPC146992
0.6176	Remote Similarity	NPC85759
0.6176	Remote Similarity	NPC478722
0.6139	Remote Similarity	NPC600446
0.6139	Remote Similarity	NPC605013
0.6117	Remote Similarity	NPC297768
0.6058	Remote Similarity	NPC307400
0.6058	Remote Similarity	NPC27289
0.6058	Remote Similarity	NPC294748
0.6019	Remote Similarity	NPC478725
0.6	Remote Similarity	NPC238264
0.6	Remote Similarity	NPC477345
0.598	Remote Similarity	NPC477326
0.5979	Remote Similarity	NPC477350
0.5962	Remote Similarity	NPC478723
0.5962	Remote Similarity	NPC478724
0.5943	Remote Similarity	NPC238056
0.5943	Remote Similarity	NPC477317
0.5943	Remote Similarity	NPC477318
0.5941	Remote Similarity	NPC604005
0.5941	Remote Similarity	NPC605014
0.5905	Remote Similarity	NPC143421
0.5842	Remote Similarity	NPC477349
0.5833	Remote Similarity	NPC123204
0.581	Remote Similarity	NPC472205
0.581	Remote Similarity	NPC477319
0.5794	Remote Similarity	NPC290012
0.575	Remote Similarity	NPC600940
0.5714	Remote Similarity	NPC475241
0.5644	Remote Similarity	NPC281563
0.5566	Remote Similarity	NPC267592
0.5514	Remote Similarity	NPC173328
0.5495	Remote Similarity	NPC269318
0.5446	Remote Similarity	NPC146380
0.5413	Remote Similarity	NPC476087
0.5413	Remote Similarity	NPC475667
0.5405	Remote Similarity	NPC163409
0.5385	Remote Similarity	NPC113745
0.5385	Remote Similarity	NPC477320
0.5385	Remote Similarity	NPC477323
0.5385	Remote Similarity	NPC477325
0.5385	Remote Similarity	NPC609436
0.5377	Remote Similarity	NPC158302
0.5364	Remote Similarity	NPC478732
0.5333	Remote Similarity	NPC611287
0.5323	Remote Similarity	NPC472352
0.5321	Remote Similarity	NPC186992
0.5315	Remote Similarity	NPC475270
0.5315	Remote Similarity	NPC475327
0.53	Remote Similarity	NPC606819
0.5289	Remote Similarity	NPC610996
0.5278	Remote Similarity	NPC479061
0.5229	Remote Similarity	NPC479060
0.5175	Remote Similarity	NPC475164
0.5081	Remote Similarity	NPC600721
0.5081	Remote Similarity	NPC605872
0.5041	Remote Similarity	NPC600672

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC290276 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4920
0.1-0.2	4135
0.2-0.3	93
0.3-0.4	2
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