NPASS Compound

Natural Product: NPC77651

Natural Product ID	NPC77651
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Purginoside Ii
IUPAC Name	n.a.
Synonyms	Purginoside II
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2336641
PubChem CID	53355580
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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1 66169 1 6 67170 1 6 68171 1 0 72172 1 0 72173 1 0 73174 1 0 73175 1 0 74176 1 0 74177 1 0 75178 1 0 75179 1 0 76180 1 0 76181 1 0 77182 1 0 77183 1 0 78184 1 0 78185 1 0 79186 1 0 79187 1 0 80188 1 0 80189 1 0 81190 1 1 83191 1 1 84192 1 6 86193 1 1 87194 1 0 88195 1 1 89196 1 1 91197 1 0 91198 1 0 91199 1 0 92200 1 0 93201 1 0 93202 1 0 94203 1 0 94204 1 0 95205 1 0 95206 1 0 96207 1 0 96208 1 0 97209 1 0 97210 1 0 97211 1 0 M END

Standard InCHIKey	MGJQNRHGDBVBKJ-KJRQEDIZSA-N
Standard InCHI	InChI=1S/C71H114O26/c1-8-11-14-15-17-21-30-37-50(75)93-66-65(97-67-56(81)54(79)53(78)47(40-72)89-67)61(95-68-58(83)62(91-51(76)39-38-45-31-26-23-27-32-45)60(43(6)85-68)90-48(73)35-25-13-10-3)44(7)87-71(66)94-59-42(5)86-70-64(57(59)82)92-49(74)36-29-22-19-16-18-20-28-34-46(33-24-12-9-2)88-69-63(96-70)55(80)52(77)41(4)84-69/h23,26-27,31-32,38-39,41-44,46-47,52-72,77-83H,8-22,24-25,28-30,33-37,40H2,1-7H3/b39-38+/t41-,42+,43+,44+,46+,47-,52+,53-,54+,55+,56-,57-,58-,59+,60+,61+,62+,63-,64-,65-,66-,67+,68+,69+,70+,71+/m1/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]1O)OC(=O)/C=C/c1ccccc1)OC(=O)CCCCC)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:	1382.76	Volume:	1384.13 ? Van der Waals volume.
Dense:	0.999	LogP:	6.046 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	5.139 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.802 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	31.0	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:	0.02	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.632	Fsp³:	0.831
MCE-18:	184.0 ? 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:	0.157 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.311 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.388	Promiscuous compounds:	0.047

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.505	MDCK Permeability:	-5.044
Pgp-inhibitor:	0.001	Pgp-substrate:	0.812
PAMPA:	0.954 ? 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):	0.011
20% Bioavailability (F20%):	0.014	30% Bioavailability (F30%):	0.956
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.929
Plasma Protein Binding (PPB):	96.491%	Volume Distribution (VD):	-0.136
Fu:	3.24% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.997
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.946

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.032
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.954 ? 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):

0.729

Half-life (T1/2):

3.644

ADMET: Toxicity

hERG Blockers:	0.073	hERG Blockers (10um):	0.148
Human Hepatotoxicity (H-HT):	0.623	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.711	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:	0.579	Drug-induced Nephrotoxicity:	0.992
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.619
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.724
BCF:	0.5 ? 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:	4.681 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.267 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.104 ? 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	=	1.4	n.a.	PMID[23273047]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FC	=	1.2	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	=	1.4	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 NPC77651 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	15162
0.1-0.2	29764
0.2-0.3	4420
0.3-0.4	367
0.4-0.5	59
0.5-0.6	36
0.6-0.7	32
0.7-0.8	0
0.8-0.85	3
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8737	High Similarity	NPC28069
0.8673	High Similarity	NPC471025
0.866	High Similarity	NPC10883
0.8469	Intermediate Similarity	NPC290276
0.8318	Intermediate Similarity	NPC147032
0.8173	Intermediate Similarity	NPC471024
0.76	Intermediate Similarity	NPC124878
0.76	Intermediate Similarity	NPC231888
0.7573	Intermediate Similarity	NPC10121
0.7573	Intermediate Similarity	NPC198918
0.7525	Intermediate Similarity	NPC35338
0.7525	Intermediate Similarity	NPC204214
0.7525	Intermediate Similarity	NPC92283
0.7477	Intermediate Similarity	NPC471026
0.7474	Intermediate Similarity	NPC162925
0.7353	Intermediate Similarity	NPC63404
0.7312	Intermediate Similarity	NPC109887
0.7065	Intermediate Similarity	NPC87153
0.6869	Remote Similarity	NPC224953
0.6667	Remote Similarity	NPC478729
0.6667	Remote Similarity	NPC477326
0.6632	Remote Similarity	NPC604005
0.6632	Remote Similarity	NPC605014
0.6495	Remote Similarity	NPC600446
0.6495	Remote Similarity	NPC605013
0.6392	Remote Similarity	NPC89843
0.6383	Remote Similarity	NPC477328
0.6383	Remote Similarity	NPC477330
0.6373	Remote Similarity	NPC183888
0.6373	Remote Similarity	NPC184915
0.6316	Remote Similarity	NPC477329
0.6286	Remote Similarity	NPC478727
0.6275	Remote Similarity	NPC169345
0.625	Remote Similarity	NPC44782
0.6238	Remote Similarity	NPC472204
0.6238	Remote Similarity	NPC119583
0.6224	Remote Similarity	NPC477331
0.6214	Remote Similarity	NPC126685
0.619	Remote Similarity	NPC478728
0.6176	Remote Similarity	NPC483170
0.617	Remote Similarity	NPC477350
0.6117	Remote Similarity	NPC115013
0.6105	Remote Similarity	NPC146380
0.6061	Remote Similarity	NPC477332
0.602	Remote Similarity	NPC113745
0.602	Remote Similarity	NPC477320
0.602	Remote Similarity	NPC477323
0.602	Remote Similarity	NPC477325
0.602	Remote Similarity	NPC609436
0.6	Remote Similarity	NPC472200
0.5979	Remote Similarity	NPC281563
0.5905	Remote Similarity	NPC259294
0.5882	Remote Similarity	NPC478722
0.5882	Remote Similarity	NPC478725
0.5865	Remote Similarity	NPC478726
0.5859	Remote Similarity	NPC22742
0.5859	Remote Similarity	NPC477349
0.5859	Remote Similarity	NPC477346
0.5842	Remote Similarity	NPC477344
0.5825	Remote Similarity	NPC478723
0.5825	Remote Similarity	NPC478724
0.5769	Remote Similarity	NPC307400
0.5769	Remote Similarity	NPC27289
0.5743	Remote Similarity	NPC478734
0.5728	Remote Similarity	NPC267592
0.5673	Remote Similarity	NPC477319
0.5631	Remote Similarity	NPC478733
0.5625	Remote Similarity	NPC606819
0.5619	Remote Similarity	NPC143421
0.5577	Remote Similarity	NPC146992
0.5577	Remote Similarity	NPC85759
0.5566	Remote Similarity	NPC238264
0.5566	Remote Similarity	NPC477345
0.5556	Remote Similarity	NPC163409
0.5556	Remote Similarity	NPC123204
0.5524	Remote Similarity	NPC297768
0.5524	Remote Similarity	NPC472205
0.5514	Remote Similarity	NPC290012
0.5514	Remote Similarity	NPC477317
0.5514	Remote Similarity	NPC477318
0.55	Remote Similarity	NPC600940
0.5472	Remote Similarity	NPC294748
0.5429	Remote Similarity	NPC479061
0.5377	Remote Similarity	NPC479060
0.537	Remote Similarity	NPC238056
0.5175	Remote Similarity	NPC475241

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC77651 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5032
0.1-0.2	4015
0.2-0.3	101
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