NPASS Compound

Natural Product: NPC69425

Natural Product ID	NPC69425
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Symplocososide E
IUPAC Name	butyl (2S,3S,4S,5R,6R)-6-[[(3S,4aR,6aR,6bS,7R,8S,8aR,9R,10R,12aS,14aR,14bR)-7,8-dihydroxy-8a-(hydroxymethyl)-4,4,6a,6b,11,11,14b-heptamethyl-9-(2-methylbutanoyloxy)-10-[(E)-3-phenylprop-2-enoyl]oxy-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-3-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-4-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylate
Synonyms	symplocososide E
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL507867
PubChem CID	21574250
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 62 14 1 0 24 17 1 0 40 27 1 0 61 56 1 0 40 22 1 0 35 28 1 0 1 89 1 0 1 90 1 0 1 91 1 0 2 92 1 0 2 93 1 0 3 94 1 0 3 95 1 0 4 96 1 0 4 97 1 0 8 98 1 1 9 99 1 6 10100 1 6 11101 1 6 12102 1 1 14103 1 1 15104 1 0 15105 1 0 16106 1 0 16107 1 0 18108 1 0 18109 1 0 18110 1 0 19111 1 1 20112 1 0 20113 1 0 21114 1 0 21115 1 0 23116 1 0 23117 1 0 23118 1 0 24119 1 1 25120 1 0 25121 1 0 26122 1 0 28123 1 1 29124 1 0 29125 1 0 31126 1 0 31127 1 0 31128 1 0 32129 1 0 32130 1 0 32131 1 0 33132 1 6 34133 1 1 36134 1 0 36135 1 0 37136 1 0 38137 1 6 39138 1 6 41139 1 0 41140 1 0 41141 1 0 42142 1 0 43143 1 0 47144 1 0 48145 1 0 48146 1 0 48147 1 0 49148 1 0 49149 1 0 50150 1 0 50151 1 0 50152 1 0 54153 1 0 55154 1 0 57155 1 0 58156 1 0 59157 1 0 60158 1 0 61159 1 0 63160 1 0 63161 1 0 63162 1 0 64163 1 0 64164 1 0 64165 1 0 67166 1 6 68167 1 1 69168 1 6 70169 1 6 71170 1 6 72171 1 0 72172 1 0 73173 1 0 75174 1 0 76175 1 0 77176 1 0 78177 1 0 80178 1 6 81179 1 1 82180 1 1 83181 1 1 84182 1 0 84183 1 0 85184 1 0 87185 1 0 88186 1 0 M END

Standard InCHIKey	BHCRZMBVGQMTHN-QIFHNBKDSA-N
Standard InCHI	InChI=1S/C65H98O23/c1-11-13-27-80-56(79)50-48(85-57-45(73)43(71)37(30-67)82-57)47(75)49(86-58-46(74)44(72)42(70)36(29-66)81-58)59(87-50)83-40-24-25-62(8)38(61(40,6)7)23-26-63(9)39(62)21-20-34-35-28-60(4,5)53(84-41(69)22-19-33-17-15-14-16-18-33)54(88-55(78)32(3)12-2)65(35,31-68)52(77)51(76)64(34,63)10/h14-20,22,32,35-40,42-54,57-59,66-68,70-77H,11-13,21,23-31H2,1-10H3/b22-19+/t32?,35-,36+,37-,38-,39+,40-,42+,43-,44-,45+,46+,47-,48-,49+,50-,51-,52+,53-,54-,57-,58-,59+,62-,63+,64-,65-/m0/s1
SMILES	CCCCOC(=O)[C@@H]1[C@H]([C@@H]([C@H]([C@H](O[C@H]2CC[C@@]3(C)[C@@H](CC[C@]4(C)[C@@H]3CC=C3[C@@H]5CC(C)(C)[C@H]([C@@H]([C@]5(CO)[C@@H]([C@@H]([C@@]43C)O)O)OC(=O)C(C)CC)OC(=O)/C=C/c3ccccc3)C2(C)C)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1246.65	Volume:	1236.871 ? Van der Waals volume.
Dense:	1.008	LogP:	3.792 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.279 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.931 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	22.0	Rigid Bonds:	53.0
TPSA:	356.81 ? Topological Polar Surface Area.	H-Bond Acceptor:	23.0
H-Bond Donor:	11.0	Rings:	9.0
Heavy Atoms:	23.0

MedChem Properties

QED Drug-Likeness Score:	0.024	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.153	Fsp³:	0.8
MCE-18:	261.427 ? 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:	0.981	Fluc inhibitor:	0.325 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.008 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.043 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.104	Promiscuous compounds:	0.053

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.273	MDCK Permeability:	-5.278
Pgp-inhibitor:	0.001	Pgp-substrate:	0.001
PAMPA:	0.997 ? 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):	0.001
20% Bioavailability (F20%):	0.885	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.905	MRP1:	0.016
Plasma Protein Binding (PPB):	83.24%	Volume Distribution (VD):	-0.437
Fu:	13.237% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.824

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.022
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.788	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.614 ? 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):

-0.006

Half-life (T1/2):

3.093

ADMET: Toxicity

hERG Blockers:	0.015	hERG Blockers (10um):	0.046
Human Hepatotoxicity (H-HT):	0.553	Drug-induced Liver Injury (DILI):	0.978
AMES Toxicity:	0.747	Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.005	Skin Sensitization:	1.0
Carcinogencity:	0.036	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.998
Hematotoxicity:	0.469	Drug-induced Nephrotoxicity:	0.993
Genotoxicity:	0.015	RPMI-8226 Immunitoxicity:	0.357
A549 Cytotoxicity:	0.929	Hek293 Cytotoxicity:	0.818
BCF:	0.509 ? 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:	3.97 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.226 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.086 ? 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
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	roots	n.a.	n.a.	PMID[15620235]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	roots	Nanning City, Guangxi Province, People's Republic of China	1997-Jan	PMID[17190442]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8121	Symplocos chinensis	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8121	Symplocos chinensis	Species	Symplocaceae	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	5

Activity Type	# Activity
Cell line	5

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
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	1700.0	nM	PMID[17190442]
NPT547	Cell line	BGC-823	Homo sapiens	IC50	>	10000.0	nM	PMID[17190442]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[17190442]
NPT179	Cell line	A2780	Homo sapiens	IC50	=	1700.0	nM	PMID[17190442]
NPT180	Cell line	HCT-8	Homo sapiens	IC50	>	10000.0	nM	PMID[17190442]

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 NPC69425 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	16699
0.1-0.2	28681
0.2-0.3	3535
0.3-0.4	735
0.4-0.5	167
0.5-0.6	24
0.6-0.7	6
0.7-0.8	0
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8655	High Similarity	NPC475513
0.8293	Intermediate Similarity	NPC173435
0.8293	Intermediate Similarity	NPC172374
0.8293	Intermediate Similarity	NPC478064
0.776	Intermediate Similarity	NPC329993
0.76	Intermediate Similarity	NPC473755
0.746	Intermediate Similarity	NPC134914
0.7364	Intermediate Similarity	NPC329657
0.6977	Remote Similarity	NPC301639
0.6977	Remote Similarity	NPC478065
0.6222	Remote Similarity	NPC475167
0.6172	Remote Similarity	NPC470914
0.6099	Remote Similarity	NPC329960
0.608	Remote Similarity	NPC478066
0.5986	Remote Similarity	NPC295408
0.5985	Remote Similarity	NPC329923
0.5985	Remote Similarity	NPC475281
0.5891	Remote Similarity	NPC470913
0.5865	Remote Similarity	NPC606553
0.5775	Remote Similarity	NPC475377
0.5775	Remote Similarity	NPC476074
0.5672	Remote Similarity	NPC329976
0.557	Remote Similarity	NPC150893
0.5461	Remote Similarity	NPC470912
0.5448	Remote Similarity	NPC111466
0.5419	Remote Similarity	NPC40085
0.5417	Remote Similarity	NPC262796
0.5417	Remote Similarity	NPC45346
0.5352	Remote Similarity	NPC46823
0.535	Remote Similarity	NPC264270
0.5315	Remote Similarity	NPC192765
0.5278	Remote Similarity	NPC178264
0.5235	Remote Similarity	NPC488309
0.517	Remote Similarity	NPC484833
0.5145	Remote Similarity	NPC477078
0.5108	Remote Similarity	NPC609281
0.5036	Remote Similarity	NPC477077
0.5035	Remote Similarity	NPC25998

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC69425 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5366
0.1-0.2	3737
0.2-0.3	47
0.3-0.4	0
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