NPASS Compound

Natural Product: NPC477466

Natural Product ID	NPC477466
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(3S,5S,6R)-6-[[(1R,2R,4S,5R,10S,13R,17S,21R,22R,23S)-21-benzoyloxy-2,23-dihydroxy-4,5,9,9,13,20,20-heptamethyl-22-(3-phenylpropanoyloxy)-24-oxahexacyclo[15.5.2.01,18.04,17.05,14.08,13]tetracosan-10-yl]oxy]-4-[(2S,3S,5R)-3-[(4S,6S)-4,5-dihydroxy-6-methyl-3-[(3S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3-hydroxy-5-[(2S,3S,5S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
IUPAC Name	(3S,5S,6R)-6-[[(1R,2R,4S,5R,10S,13R,17S,21R,22R,23S)-21-benzoyloxy-2,23-dihydroxy-4,5,9,9,13,20,20-heptamethyl-22-(3-phenylpropanoyloxy)-24-oxahexacyclo[15.5.2.01,18.04,17.05,14.08,13]tetracosan-10-yl]oxy]-4-[(2S,3S,5R)-3-[(4S,6S)-4,5-dihydroxy-6-methyl-3-[(3S,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3-hydroxy-5-[(2S,3S,5S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44388620
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

RDKit 3D 218230 0 0 0 0 0 0 0 0999 V2000 -12.6444 2.1346 -2.1478 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.0091 3.5012 -2.3143 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.9753 4.6223 -2.1192 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.6078 5.3579 -0.8460 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.2402 4.3623 0.2390 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.1109 3.4755 -0.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8730 3.6919 -1.5525 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.4196 2.1693 0.1297 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.5840 1.6729 1.1066 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2979 1.4788 2.4272 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.6192 -0.0006 2.6689 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3228 -0.7963 2.6251 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.3095 -0.0228 2.0399 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.7993 0.4690 0.7774 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6421 0.6888 0.0140 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5588 -0.3227 -0.9394 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2883 -1.1382 -0.7475 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2113 -2.0848 -1.7301 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0751 -1.6866 -3.0175 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1763 -0.7123 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Standard InCHIKey	VLECVQIWMOLKCA-AZBJESKUSA-N
Standard InCHI	InChI=1S/C76H110O32/c1-32-44(81)48(85)52(89)64(96-32)104-57-50(87)45(82)33(2)97-66(57)105-58-51(88)47(84)37(31-78)99-67(58)102-55-54(91)56(62(92)93)103-68(59(55)106-65-53(90)49(86)46(83)36(30-77)98-65)100-42-24-25-72(7)38(71(42,5)6)22-26-73(8)39(72)23-27-75-40-28-70(3,4)60(107-63(94)35-18-14-11-15-19-35)61(101-43(80)21-20-34-16-12-10-13-17-34)76(40,69(95)108-75)41(79)29-74(73,75)9/h10-19,32-33,36-42,44-61,64-69,77-79,81-91,95H,20-31H2,1-9H3,(H,92,93)/t32-,33-,36?,37?,38?,39?,40?,41+,42-,44-,45?,46+,47-,48?,49?,50-,51?,52-,53-,54-,55?,56?,57?,58-,59-,60-,61-,64?,65-,66?,67-,68+,69-,72-,73+,74-,75-,76+/m0/s1
SMILES	C[C@H]1[C@@H](C([C@@H](C(O1)OC2[C@H](C([C@@H](OC2O[C@@H]3[C@@H](OC([C@@H](C3O)O)CO)OC4[C@@H]([C@@H](OC([C@H]4O)C(=O)O)O[C@H]5CC[C@@]6(C7CC[C@]89C1CC([C@H]([C@@H]([C@@]1([C@@H](C[C@]8([C@@]7(CCC6C5(C)C)C)C)O)[C@H](O9)O)OC(=O)CCC1=CC=CC=C1)OC(=O)C1=CC=CC=C1)(C)C)C)O[C@H]1[C@H](C([C@@H](C(O1)CO)O)O)O)C)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1534.7	Volume:	1469.377 ? Van der Waals volume.
Dense:	1.044	LogP:	0.629 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.494 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.0 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	21.0	Rigid Bonds:	74.0
TPSA:	494.88 ? Topological Polar Surface Area.	H-Bond Acceptor:	32.0
H-Bond Donor:	16.0	Rings:	13.0
Heavy Atoms:	32.0

MedChem Properties

QED Drug-Likeness Score:	0.059	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	8.159	Fsp³:	0.803
MCE-18:	460.672 ? 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:	0.694	Fluc inhibitor:	0.002 ? 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:	0.334 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.352	Promiscuous compounds:	0.042

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.536	MDCK Permeability:	-5.135
Pgp-inhibitor:	0.0	Pgp-substrate:	0.998
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):	0.0
20% Bioavailability (F20%):	0.055	30% Bioavailability (F30%):	0.641
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.874
Plasma Protein Binding (PPB):	71.028%	Volume Distribution (VD):	-0.534
Fu:	22.157% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.975
OATP1B3 inhibitor:	0.389	BCRP inhibitor:	0.0
BSEP inhibitor:	0.002

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:	0.001 ? 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):

-1.026

Half-life (T1/2):

5.532

ADMET: Toxicity

hERG Blockers:	0.004	hERG Blockers (10um):	0.07
Human Hepatotoxicity (H-HT):	0.342	Drug-induced Liver Injury (DILI):	0.454
AMES Toxicity:	0.676	Rat Oral Acute Toxicity:	0.013
Maximum Recommended Daily Dose:	0.038	Skin Sensitization:	0.999
Carcinogencity:	0.011	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.024	Drug-induced Nephrotoxicity:	0.98
Genotoxicity:	0.027	RPMI-8226 Immunitoxicity:	0.219
A549 Cytotoxicity:	0.33	Hek293 Cytotoxicity:	0.792
BCF:	0.024 ? 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:	3.887 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.24 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.503 ? 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
NPO22350	Maesa balansae	Species	Primulaceae	Eukaryota	Leaves	Deo Khe, Dai Tu district, Thai Nguyen province in Vietnam	2000-NOV	PMID[15633999]
NPO22350	Maesa balansae	Species	Primulaceae	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
IC90	1
CC50	1

Activity Type	# Activity
Cell line	1
Organism	2

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
NPT171	Cell line	MRC5	Homo sapiens	CC50	=	0.3	ug/ml	PMID[15633999]
NPT1021	Organism	Leishmania infantum	Leishmania infantum	IC50	=	0.009	ug/ml	PMID[15633999]
NPT1021	Organism	Leishmania infantum	Leishmania infantum	IC90	=	0.015	ug/ml	PMID[15633999]

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 NPC477466 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	18425
0.1-0.2	27906
0.2-0.3	2883
0.3-0.4	533
0.4-0.5	94
0.5-0.6	7
0.6-0.7	2
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8955	High Similarity	NPC477467
0.8561	High Similarity	NPC477469
0.8561	High Similarity	NPC477471
0.7708	Intermediate Similarity	NPC477470
0.7708	Intermediate Similarity	NPC477472
0.7432	Intermediate Similarity	NPC477473
0.6732	Remote Similarity	NPC477474
0.6642	Remote Similarity	NPC477465
0.5298	Remote Similarity	NPC46823
0.5226	Remote Similarity	NPC484059
0.5226	Remote Similarity	NPC484060
0.513	Remote Similarity	NPC484061
0.513	Remote Similarity	NPC484062
0.5098	Remote Similarity	NPC277212
0.5098	Remote Similarity	NPC30279

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC477466 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4794
0.1-0.2	4304
0.2-0.3	51
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