NPASS Compound

Natural Product: NPC475177

Natural Product ID	NPC475177
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-O-{Alpha-L-Arabinopyranosyl(1->6)-[Beta-D-Glucopyranosyl(1->2)]-Beta-D-Glucopyranosyl}-21-O-[(2E)-6-Hydroxyl-2-Hydroxymethyl-6-Methyl-2,7-Octadienoyl]Acacic Acid 28-O-Alpha-L-Arabinofuranosyl(1->4)-[Beta-D-Glucopyranosyl(1->3)]-A Lpha-L-Rhamnopyranosyl(1->2)-Beta-D-Glucopyranosyl Ester
IUPAC Name	[(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5S,6S)-5-[(2R,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-6-methyl-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl] (3S,4aR,5R,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-[[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxymethyl]oxan-2-yl]oxy-5-hydroxy-3-[(2E)-6-hydroxy-2-(hydroxymethyl)-6-methylocta-2,7-dienoyl]oxy-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	CHEMBL500180
PubChem CID	44566292
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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62185 1 0 63186 1 0 64187 1 0 66188 1 0 67189 1 0 68190 1 0 69191 1 0 70192 1 0 72193 1 0 72194 1 0 73195 1 0 74196 1 0 75197 1 0 76198 1 0 77199 1 0 77200 1 0 77201 1 0 78202 1 0 78203 1 0 78204 1 0 79205 1 0 79206 1 0 79207 1 0 84208 1 0 85209 1 0 85210 1 0 86211 1 0 86212 1 0 88213 1 0 88214 1 0 88215 1 0 89216 1 0 90217 1 0 90218 1 0 91219 1 0 92220 1 0 92221 1 0 93222 1 0 94223 1 0 94224 1 0 95225 1 0 96226 1 0 97227 1 0 98228 1 0 100229 1 0 101230 1 0 102231 1 0 103232 1 0 104233 1 0 106234 1 0 106235 1 0 107236 1 0 108237 1 0 109238 1 0 110239 1 0 112240 1 0 113241 1 0 114242 1 0 115243 1 0 117244 1 0 117245 1 0 118246 1 0 119247 1 0 120248 1 0 M END

Standard InCHIKey	VMHSOXVWGGXLLL-XRZHIYRZSA-N
Standard InCHI	InChI=1S/C80H128O40/c1-11-76(7,105)18-12-13-32(24-81)65(103)114-45-23-80(73(104)120-72-64(54(96)49(91)38(27-84)112-72)119-70-60(102)62(117-68-58(100)52(94)47(89)36(25-82)109-68)61(31(2)108-70)116-67-57(99)50(92)39(28-85)111-67)34(21-74(45,3)4)33-14-15-42-77(8)19-17-44(75(5,6)41(77)16-20-78(42,9)79(33,10)22-43(80)87)115-71-63(118-69-59(101)53(95)48(90)37(26-83)110-69)55(97)51(93)40(113-71)30-107-66-56(98)46(88)35(86)29-106-66/h11,13-14,31,34-64,66-72,81-102,105H,1,12,15-30H2,2-10H3/b32-13+/t31-,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+,66-,67+,68-,69-,70-,71-,72-,76?,77-,78+,79+,80+/m0/s1
SMILES	CC1C(C(C(C(O1)OC2C(C(C(OC2OC(=O)C34CC(C(CC3C5=CCC6C7(CCC(C(C7CCC6(C5(CC4O)C)C)(C)C)OC8C(C(C(C(O8)COC9C(C(C(CO9)O)O)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)C)(C)C)OC(=O)C(=CCCC(C)(C=C)O)CO)CO)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)OC1C(C(C(O1)CO)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1728.8	Volume:	1627.985 ? Van der Waals volume.
Dense:	1.062	LogP:	-2.174 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.953 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.547 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	28.0	Rigid Bonds:	71.0
TPSA:	637.88 ? Topological Polar Surface Area.	H-Bond Acceptor:	40.0
H-Bond Donor:	23.0	Rings:	12.0
Heavy Atoms:	40.0

MedChem Properties

QED Drug-Likeness Score:	0.017	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.886	Fsp³:	0.9
MCE-18:	271.053 ? 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:	0.0	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.478 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.445	Promiscuous compounds:	0.001

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.38	MDCK Permeability:	-4.922
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):	1.0
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	12.639%	Volume Distribution (VD):	-0.363
Fu:	34.029% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.026	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.072	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.005	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.0 ? 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):

-1.806

Half-life (T1/2):

5.099

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.06
Human Hepatotoxicity (H-HT):	0.221	Drug-induced Liver Injury (DILI):	0.11
AMES Toxicity:	0.665	Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.03	Skin Sensitization:	0.017
Carcinogencity:	0.001	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.148	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.006
Genotoxicity:	0.004	RPMI-8226 Immunitoxicity:	0.161
A549 Cytotoxicity:	0.003	Hek293 Cytotoxicity:	0.959
BCF:	-0.115 ? 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:	4.078 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.747 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.329 ? 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
NPO3615	Acacia concinna	Species	Fabaceae	Eukaryota	fruits	myanmar	n.a.	PMID[11141109]
NPO3615	Acacia concinna	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3615	Acacia concinna	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
ED50	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
NPT453	Cell line	HT-1080	Homo sapiens	ED50	=	0.91	uM	PubChem BioAssay data set

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 NPC475177 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	23986
0.1-0.2	22228
0.2-0.3	2545
0.3-0.4	654
0.4-0.5	341
0.5-0.6	56
0.6-0.7	20
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.903	High Similarity	NPC475444
0.903	High Similarity	NPC473679
0.8846	High Similarity	NPC484830
0.8116	Intermediate Similarity	NPC196874
0.7883	Intermediate Similarity	NPC484831
0.7867	Intermediate Similarity	NPC174336
0.7662	Intermediate Similarity	NPC187497
0.766	Intermediate Similarity	NPC233223
0.766	Intermediate Similarity	NPC183816
0.7606	Intermediate Similarity	NPC300655
0.7603	Intermediate Similarity	NPC113620
0.7589	Intermediate Similarity	NPC484829
0.7568	Intermediate Similarity	NPC322904
0.755	Intermediate Similarity	NPC488201
0.75	Intermediate Similarity	NPC100612
0.7467	Intermediate Similarity	NPC319719
0.7397	Intermediate Similarity	NPC222951
0.7343	Intermediate Similarity	NPC329878
0.7241	Intermediate Similarity	NPC13989
0.7172	Intermediate Similarity	NPC43589
0.7143	Intermediate Similarity	NPC488204
0.7083	Intermediate Similarity	NPC329893
0.7059	Intermediate Similarity	NPC324933
0.698	Remote Similarity	NPC311178
0.6859	Remote Similarity	NPC265699
0.6744	Remote Similarity	NPC207738
0.6711	Remote Similarity	NPC220838
0.6709	Remote Similarity	NPC488202
0.6709	Remote Similarity	NPC488200
0.6667	Remote Similarity	NPC488620
0.6645	Remote Similarity	NPC478559
0.6645	Remote Similarity	NPC478560
0.6558	Remote Similarity	NPC23020
0.6335	Remote Similarity	NPC488203
0.6316	Remote Similarity	NPC45606
0.6296	Remote Similarity	NPC123522
0.617	Remote Similarity	NPC470876
0.6164	Remote Similarity	NPC489209
0.6133	Remote Similarity	NPC489208
0.6125	Remote Similarity	NPC472270
0.6125	Remote Similarity	NPC112492
0.6101	Remote Similarity	NPC482013
0.6038	Remote Similarity	NPC488619
0.5986	Remote Similarity	NPC286457
0.5975	Remote Similarity	NPC488618
0.5974	Remote Similarity	NPC472268
0.5909	Remote Similarity	NPC105800
0.5882	Remote Similarity	NPC104137
0.5882	Remote Similarity	NPC26626
0.585	Remote Similarity	NPC482010
0.5833	Remote Similarity	NPC232237
0.5822	Remote Similarity	NPC309223
0.5762	Remote Similarity	NPC33012
0.5745	Remote Similarity	NPC603137
0.5695	Remote Similarity	NPC8524
0.5683	Remote Similarity	NPC172365
0.5683	Remote Similarity	NPC185466
0.5625	Remote Similarity	NPC85154
0.5612	Remote Similarity	NPC210729
0.5612	Remote Similarity	NPC82931
0.5563	Remote Similarity	NPC102505
0.5563	Remote Similarity	NPC488514
0.5548	Remote Similarity	NPC473452
0.5548	Remote Similarity	NPC13998
0.5507	Remote Similarity	NPC481079
0.5506	Remote Similarity	NPC297950
0.543	Remote Similarity	NPC220160
0.5423	Remote Similarity	NPC610204
0.5422	Remote Similarity	NPC472269
0.5402	Remote Similarity	NPC488513
0.5396	Remote Similarity	NPC291903
0.5385	Remote Similarity	NPC1046
0.5368	Remote Similarity	NPC164389
0.5274	Remote Similarity	NPC283417
0.5274	Remote Similarity	NPC200049
0.5274	Remote Similarity	NPC475140
0.5263	Remote Similarity	NPC70809
0.5259	Remote Similarity	NPC469946
0.5223	Remote Similarity	NPC480421
0.5202	Remote Similarity	NPC475599
0.518	Remote Similarity	NPC488517
0.513	Remote Similarity	NPC482011
0.5114	Remote Similarity	NPC475527
0.5106	Remote Similarity	NPC470914
0.5103	Remote Similarity	NPC473824
0.5103	Remote Similarity	NPC610461
0.5102	Remote Similarity	NPC609305
0.5096	Remote Similarity	NPC480422
0.5072	Remote Similarity	NPC30289
0.5071	Remote Similarity	NPC470514
0.5071	Remote Similarity	NPC123796
0.5069	Remote Similarity	NPC815
0.5069	Remote Similarity	NPC606553
0.5067	Remote Similarity	NPC57484
0.5036	Remote Similarity	NPC488526
0.5035	Remote Similarity	NPC64715
0.5034	Remote Similarity	NPC475119
0.5033	Remote Similarity	NPC265841
0.5033	Remote Similarity	NPC480418

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC475177 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7778
0.1-0.2	1332
0.2-0.3	36
0.3-0.4	4
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