NPASS Compound

Natural Product: NPC475152

Natural Product ID	NPC475152
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3Beta-O-{Beta-D-Xylopyranosyl-(1->3)-Alpha-L-Arabinopyranosyl-(1->6)-[Beta-D-Glucopyranosyl-(1->4)]-2-(Acetamido)-2-Deoxy-Beta-D-Glucopyranosyl}Echinocystic Acid 28-O-Beta-D-Apiofuranosyl-(1->3)-Beta-D-Xylopyranosyl-(1->2)-[(-Beta-D-Xylopyranosyl-(1->4)]-(6-O-Acetyl)-Beta-D-Glucopyranosyl Ester
IUPAC Name	[(2S,3R,4S,5R,6R)-6-(acetyloxymethyl)-3-[(2S,3R,4S,5R)-4-[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy-3,5-dihydroxyoxan-2-yl]oxy-5-hydroxy-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl] (4aR,5R,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4R,5S,6R)-3-acetamido-6-[[(2S,3R,4S,5S)-3,5-dihydroxy-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxymethyl]-4-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-5-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL499449
PubChem CID	44566573
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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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95214 1 0 96215 1 0 96216 1 0 97217 1 0 98218 1 0 100219 1 6 102220 1 0 102221 1 0 103222 1 1 104223 1 6 105224 1 1 106225 1 0 107226 1 0 108227 1 0 109228 1 0 110229 1 0 111230 1 0 111231 1 0 111232 1 0 112233 1 0 112234 1 0 112235 1 0 113236 1 1 114237 1 6 115238 1 1 116239 1 0 117240 1 0 118241 1 0 M END

Standard InCHIKey	TYZQUEGBQIPUMH-MTABPQSOSA-N
Standard InCHI	InChI=1S/C77H123NO40/c1-29(81)78-44-49(92)58(115-67-53(96)50(93)47(90)37(20-79)109-67)39(26-107-63-54(97)56(35(85)23-103-63)113-64-51(94)45(88)33(83)21-104-64)111-62(44)112-43-13-14-73(7)40(72(43,5)6)12-15-74(8)41(73)11-10-31-32-18-71(3,4)16-17-77(32,42(87)19-75(31,74)9)70(100)118-68-60(117-66-55(98)57(36(86)24-106-66)114-69-61(99)76(101,27-80)28-108-69)59(48(91)38(110-68)25-102-30(2)82)116-65-52(95)46(89)34(84)22-105-65/h10,32-69,79-80,83-99,101H,11-28H2,1-9H3,(H,78,81)/t32-,33+,34+,35-,36+,37+,38+,39+,40-,41+,42+,43-,44+,45-,46-,47+,48+,49+,50-,51+,52+,53+,54+,55+,56-,57-,58+,59-,60+,61-,62-,63-,64-,65-,66-,67-,68-,69-,73-,74+,75+,76+,77+/m0/s1
SMILES	OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO[C@@H]3OC[C@@H]([C@@H]([C@H]3O)O[C@@H]3OC[C@H]([C@@H]([C@H]3O)O)O)O)O[C@H]([C@@H]([C@H]2O)N=C(O)C)O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3CC=C3[C@@]2(C)C[C@H]([C@@]2([C@H]3CC(C)(C)CC2)C(=O)O[C@@H]2O[C@H](COC(=O)C)[C@H]([C@@H]([C@H]2O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O[C@@H]2OC[C@]([C@H]2O)(O)CO)O)O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)O)O)C)C)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1701.76	Volume:	1581.173 ? Van der Waals volume.
Dense:	1.076	LogP:	-0.042 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.873 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.838 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	24.0	Rigid Bonds:	76.0
TPSA:	628.24 ? Topological Polar Surface Area.	H-Bond Acceptor:	41.0
H-Bond Donor:	21.0	Rings:	13.0
Heavy Atoms:	41.0

MedChem Properties

QED Drug-Likeness Score:	0.016	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.88	Fsp³:	0.935
MCE-18:	284.779 ? 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:	0.699	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.267	Promiscuous compounds:	0.415

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.186	MDCK Permeability:	-5.011
Pgp-inhibitor:	0.0	Pgp-substrate:	1.0
PAMPA:	1.0 ? 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):	0.803
20% Bioavailability (F20%):	0.436	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.002
Plasma Protein Binding (PPB):	43.484%	Volume Distribution (VD):	-0.449
Fu:	33.481% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

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:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.002 ? 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):

-1.481

Half-life (T1/2):

4.329

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.996	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.006	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.644	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.492	RPMI-8226 Immunitoxicity:	0.339
A549 Cytotoxicity:	0.874	Hek293 Cytotoxicity:	0.254
BCF:	0.346 ? 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:	3.361 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.259 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.802 ? 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
NPO11507	Entada africana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16989528]
NPO11507	Entada africana	Species	Fabaceae	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	1

Activity Type	# Activity
Cell line	1

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
NPT1182	Cell line	J774.A1	Mus musculus	IC50	=	2900.0	nM	PMID[23507152]

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 NPC475152 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	24969
0.1-0.2	21775
0.2-0.3	2205
0.3-0.4	523
0.4-0.5	288
0.5-0.6	71
0.6-0.7	13
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC475584
0.8716	High Similarity	NPC476113
0.7724	Intermediate Similarity	NPC475892
0.7655	Intermediate Similarity	NPC475394
0.7564	Intermediate Similarity	NPC475527
0.741	Intermediate Similarity	NPC475649
0.7044	Intermediate Similarity	NPC475599
0.6972	Remote Similarity	NPC482010
0.6761	Remote Similarity	NPC475345
0.6667	Remote Similarity	NPC489208
0.6486	Remote Similarity	NPC489209
0.6408	Remote Similarity	NPC85154
0.6184	Remote Similarity	NPC33012
0.6174	Remote Similarity	NPC482011
0.6149	Remote Similarity	NPC302543
0.6118	Remote Similarity	NPC8524
0.6096	Remote Similarity	NPC13998
0.6053	Remote Similarity	NPC153673
0.604	Remote Similarity	NPC144644
0.604	Remote Similarity	NPC170407
0.5987	Remote Similarity	NPC68767
0.596	Remote Similarity	NPC142151
0.5948	Remote Similarity	NPC110385
0.5948	Remote Similarity	NPC51099
0.5935	Remote Similarity	NPC275225
0.5933	Remote Similarity	NPC309223
0.5933	Remote Similarity	NPC482012
0.5933	Remote Similarity	NPC37860
0.5931	Remote Similarity	NPC283417
0.5931	Remote Similarity	NPC200049
0.5882	Remote Similarity	NPC102505
0.5882	Remote Similarity	NPC293031
0.5882	Remote Similarity	NPC488514
0.5855	Remote Similarity	NPC220160
0.5855	Remote Similarity	NPC267694
0.5843	Remote Similarity	NPC23020
0.5839	Remote Similarity	NPC475514
0.5833	Remote Similarity	NPC480421
0.5818	Remote Similarity	NPC485563
0.5775	Remote Similarity	NPC104137
0.5775	Remote Similarity	NPC26626
0.5758	Remote Similarity	NPC1046
0.5734	Remote Similarity	NPC11242
0.5652	Remote Similarity	NPC117714
0.5652	Remote Similarity	NPC30289
0.5638	Remote Similarity	NPC4749
0.5556	Remote Similarity	NPC481081
0.551	Remote Similarity	NPC123522
0.5506	Remote Similarity	NPC480422
0.55	Remote Similarity	NPC164389
0.5461	Remote Similarity	NPC286457
0.5425	Remote Similarity	NPC470876
0.5396	Remote Similarity	NPC263756
0.5396	Remote Similarity	NPC213674
0.5395	Remote Similarity	NPC21691
0.5376	Remote Similarity	NPC472270
0.5376	Remote Similarity	NPC112492
0.5306	Remote Similarity	NPC210729
0.5306	Remote Similarity	NPC82931
0.5287	Remote Similarity	NPC70809
0.5286	Remote Similarity	NPC76497
0.5278	Remote Similarity	NPC64715
0.527	Remote Similarity	NPC172365
0.526	Remote Similarity	NPC472269
0.5252	Remote Similarity	NPC173583
0.5238	Remote Similarity	NPC207738
0.5238	Remote Similarity	NPC187290
0.5232	Remote Similarity	NPC123199
0.5202	Remote Similarity	NPC488619
0.5195	Remote Similarity	NPC473386
0.518	Remote Similarity	NPC475516
0.5175	Remote Similarity	NPC488526
0.5163	Remote Similarity	NPC488560
0.5163	Remote Similarity	NPC471577
0.5143	Remote Similarity	NPC113620
0.5135	Remote Similarity	NPC481078
0.5125	Remote Similarity	NPC250247
0.5099	Remote Similarity	NPC79643
0.5098	Remote Similarity	NPC475160
0.5098	Remote Similarity	NPC473714
0.5085	Remote Similarity	NPC100612
0.5068	Remote Similarity	NPC69811
0.5067	Remote Similarity	NPC185466
0.5064	Remote Similarity	NPC473452
0.5062	Remote Similarity	NPC224381
0.5056	Remote Similarity	NPC265699
0.5056	Remote Similarity	NPC488620
0.5033	Remote Similarity	NPC610204
0.5032	Remote Similarity	NPC41061
0.5032	Remote Similarity	NPC227551
0.5032	Remote Similarity	NPC481080

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC475152 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7289
0.1-0.2	1828
0.2-0.3	32
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