NPASS Compound

Natural Product: NPC477470

Natural Product ID	NPC477470
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)-2,23-dihydroxy-4,5,9,9,13,20,20-heptamethyl-21-[(Z)-2-methylbut-2-enoyl]oxy-22-[(Z)-3-phenylprop-2-enoyl]oxy-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)-2,23-dihydroxy-4,5,9,9,13,20,20-heptamethyl-21-[(Z)-2-methylbut-2-enoyl]oxy-22-[(Z)-3-phenylprop-2-enoyl]oxy-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	44388717
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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0 26134 1 0 27135 1 0 27136 1 0 27137 1 0 29138 1 1 30139 1 0 31140 1 0 31141 1 0 32142 1 0 32143 1 0 33144 1 6 35145 1 0 35146 1 0 35147 1 0 36148 1 0 36149 1 0 36150 1 0 38151 1 6 39152 1 6 40153 1 0 41154 1 1 42155 1 0 46156 1 0 47157 1 0 49158 1 6 50159 1 1 51160 1 0 52161 1 1 53162 1 0 55163 1 0 55164 1 0 56165 1 0 57166 1 0 58167 1 0 60168 1 0 61169 1 0 62170 1 6 63171 1 0 64172 1 6 66173 1 0 66174 1 0 66175 1 0 67176 1 0 68177 1 0 70178 1 0 71179 1 6 72180 1 0 73181 1 6 74182 1 1 76183 1 0 76184 1 0 76185 1 0 77186 1 0 78187 1 0 79188 1 0 81189 1 6 82190 1 1 83191 1 0 84192 1 1 85193 1 0 87194 1 0 87195 1 0 88196 1 0 89197 1 0 90198 1 0 91199 1 0 92200 1 0 92201 1 0 92202 1 0 93203 1 0 93204 1 0 93205 1 0 94206 1 0 94207 1 0 94208 1 0 95209 1 0 99210 1 0 100211 1 0 102212 1 0 103213 1 0 104214 1 0 105215 1 0 106216 1 0 M END

Standard InCHIKey	JFWFXEOYRZGWQD-UKENCKCSSA-N
Standard InCHI	InChI=1S/C74H110O32/c1-12-30(2)61(92)105-58-59(99-41(78)19-18-33-16-14-13-15-17-33)74-38(26-68(58,5)6)73(106-67(74)93)25-21-37-70(9)23-22-40(69(7,8)36(70)20-24-71(37,10)72(73,11)27-39(74)77)98-66-57(104-63-51(88)47(84)44(81)34(28-75)96-63)53(52(89)54(101-66)60(90)91)100-65-56(49(86)45(82)35(29-76)97-65)103-64-55(48(85)43(80)32(4)95-64)102-62-50(87)46(83)42(79)31(3)94-62/h12-19,31-32,34-40,42-59,62-67,75-77,79-89,93H,20-29H2,1-11H3,(H,90,91)/b19-18-,30-12-/t31-,32-,34?,35?,36?,37?,38?,39+,40-,42-,43?,44+,45-,46?,47?,48-,49?,50-,51-,52-,53?,54?,55?,56-,57-,58-,59-,62?,63-,64?,65-,66+,67-,70-,71+,72-,73-,74+/m0/s1
SMILES	C/C=C(/C)\C(=O)O[C@H]1[C@@H]([C@]23[C@@H](C[C@]4([C@@]5(CCC6[C@@](C5CC[C@@]4(C2CC1(C)C)O[C@@H]3O)(CC[C@@H](C6(C)C)O[C@H]7[C@H](C([C@@H](C(O7)C(=O)O)O)O[C@H]8[C@H](C([C@H](C(O8)CO)O)O)OC9C([C@H](C([C@@H](O9)C)O)O)OC1[C@H](C([C@H]([C@@H](O1)C)O)O)O)O[C@H]1[C@H](C([C@@H](C(O1)CO)O)O)O)C)C)C)O)OC(=O)/C=C\C1=CC=CC=C1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1510.7	Volume:	1445.977 ? Van der Waals volume.
Dense:	1.045	LogP:	0.909 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.069 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.679 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	20.0	Rigid Bonds:	70.0
TPSA:	494.88 ? Topological Polar Surface Area.	H-Bond Acceptor:	32.0
H-Bond Donor:	16.0	Rings:	12.0
Heavy Atoms:	32.0

MedChem Properties

QED Drug-Likeness Score:	0.046	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	8.227	Fsp³:	0.824
MCE-18:	447.556 ? 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:	0.328 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.023 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.341 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.359	Promiscuous compounds:	0.023

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.385	MDCK Permeability:	-5.243
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):	0.999
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:	0.999
Plasma Protein Binding (PPB):	61.953%	Volume Distribution (VD):	-0.535
Fu:	26.658% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.962
OATP1B3 inhibitor:	0.175	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:	0.02	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.001
HLM stability:	0.007 ? 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):

-0.93

Half-life (T1/2):

4.242

ADMET: Toxicity

hERG Blockers:	0.001	hERG Blockers (10um):	0.003
Human Hepatotoxicity (H-HT):	0.62	Drug-induced Liver Injury (DILI):	0.237
AMES Toxicity:	0.894	Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.049	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.003
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.054	Drug-induced Nephrotoxicity:	0.985
Genotoxicity:	0.007	RPMI-8226 Immunitoxicity:	0.481
A549 Cytotoxicity:	0.989	Hek293 Cytotoxicity:	0.85
BCF:	0.042 ? 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:	3.827 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.216 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.636 ? 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	=	0.5	ug/ml	PMID[15633999]
NPT1021	Organism	Leishmania infantum	Leishmania infantum	IC50	=	0.023	ug/ml	PMID[15633999]
NPT1021	Organism	Leishmania infantum	Leishmania infantum	IC90	=	0.094	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 NPC477470 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	17306
0.1-0.2	28894
0.2-0.3	2930
0.3-0.4	567
0.4-0.5	135
0.5-0.6	18
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC477472
0.9037	High Similarity	NPC477469
0.9037	High Similarity	NPC477471
0.875	High Similarity	NPC477474
0.8603	High Similarity	NPC477467
0.7847	Intermediate Similarity	NPC477473
0.7708	Intermediate Similarity	NPC477466
0.6691	Remote Similarity	NPC477465
0.5972	Remote Similarity	NPC46823
0.5878	Remote Similarity	NPC484059
0.5878	Remote Similarity	NPC484060
0.5676	Remote Similarity	NPC484061
0.5676	Remote Similarity	NPC484062
0.5646	Remote Similarity	NPC277212
0.5646	Remote Similarity	NPC30279
0.5325	Remote Similarity	NPC329657
0.5321	Remote Similarity	NPC484063
0.5321	Remote Similarity	NPC484064
0.5238	Remote Similarity	NPC25998
0.5205	Remote Similarity	NPC329976
0.5132	Remote Similarity	NPC473918
0.5098	Remote Similarity	NPC192765
0.5098	Remote Similarity	NPC329828
0.5097	Remote Similarity	NPC271610
0.5097	Remote Similarity	NPC225791
0.5065	Remote Similarity	NPC178264

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC477470 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5122
0.1-0.2	3992
0.2-0.3	34
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