NPASS Compound

Natural Product: NPC13989

Natural Product ID	NPC13989
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Adianthifolioside B
IUPAC Name	[(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5S,6S)-5-[(2S,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)-6-[[(2R,3R,4S,5R,6R)-4,5-dihydroxy-6-methyl-3-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxymethyl]-4,5-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-5-hydroxy-3-(2-hydroxybenzoyl)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	Adianthifolioside B
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL507216
PubChem CID	21629543
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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59 1 0 59 60 1 0 60 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 65 68 1 0 64 69 1 0 58 70 1 0 57 71 1 0 50 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 75 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 79 80 1 0 78 81 1 0 81 82 1 0 82 83 1 0 83 84 1 0 82 85 1 0 81 86 1 0 73 87 1 0 72 88 1 0 22 89 1 0 22 90 1 0 5 91 1 0 91 92 1 0 92 93 1 0 93 94 1 0 92 95 1 0 91 96 1 0 96 97 1 0 97 98 1 0 98 99 1 0 99100 1 0 99101 1 0 101102 1 0 102103 1 0 103104 1 0 102105 1 0 105106 1 0 106107 1 0 107108 1 0 108109 1 0 109110 1 0 108111 1 0 111112 1 0 112113 1 0 113114 1 0 112115 1 0 111116 1 0 101117 1 0 117118 1 0 118119 1 0 119120 1 0 120121 1 0 121122 1 0 122123 1 0 121124 1 0 120125 1 0 125126 1 0 93 3 1 0 103 97 1 0 113106 1 0 122118 1 0 32 9 1 0 44 38 1 0 74 48 1 0 83 76 1 0 24 9 1 0 30 25 1 0 59 53 1 0 66 61 1 0 20 15 1 0 39 28 1 0 1127 1 0 2128 1 0 2129 1 0 3130 1 1 5131 1 1 10132 1 0 10133 1 0 11134 1 6 16135 1 0 17136 1 0 18137 1 0 19138 1 0 21139 1 0 23140 1 0 23141 1 0 24142 1 1 26143 1 0 27144 1 0 27145 1 0 28146 1 6 31147 1 0 31148 1 0 32149 1 1 33150 1 0 34151 1 0 34152 1 0 34153 1 0 35154 1 0 35155 1 0 35156 1 0 36157 1 0 36158 1 0 37159 1 0 37160 1 0 38161 1 6 40162 1 0 40163 1 0 40164 1 0 41165 1 0 41166 1 0 42167 1 0 42168 1 0 43169 1 6 45170 1 0 45171 1 0 45172 1 0 46173 1 0 46174 1 0 46175 1 0 48176 1 1 50177 1 1 51178 1 0 51179 1 0 53180 1 6 55181 1 6 56182 1 0 56183 1 0 56184 1 0 57185 1 6 58186 1 6 59187 1 1 61188 1 6 63189 1 0 63190 1 0 64191 1 1 65192 1 6 66193 1 1 67194 1 0 68195 1 0 69196 1 0 70197 1 0 71198 1 0 72199 1 6 73200 1 1 74201 1 6 76202 1 1 78203 1 1 79204 1 0 79205 1 0 80206 1 0 81207 1 6 82208 1 1 83209 1 6 84210 1 0 85211 1 0 86212 1 0 87213 1 0 88214 1 0 89215 1 0 89216 1 0 89217 1 0 90218 1 0 90219 1 0 90220 1 0 91221 1 6 92222 1 1 93223 1 6 94224 1 0 95225 1 0 97226 1 1 99227 1 6 100228 1 0 100229 1 0 100230 1 0 101231 1 1 102232 1 6 103233 1 6 104234 1 0 106235 1 6 108236 1 6 109237 1 0 109238 1 0 110239 1 0 111240 1 1 112241 1 6 113242 1 1 114243 1 0 115244 1 0 116245 1 0 118246 1 6 120247 1 1 121248 1 6 122249 1 1 123250 1 0 124251 1 0 125252 1 0 125253 1 0 126254 1 0 M END

Standard InCHIKey	LSDHKFVHNGZFOG-GWCHSLTQSA-N
Standard InCHI	InChI=1S/C83H128O43/c1-29-46(91)55(100)65(123-69-58(103)47(92)35(89)27-110-69)74(112-29)111-28-40-52(97)57(102)66(124-72-61(106)54(99)49(94)37(24-85)115-72)75(118-40)120-44-17-18-80(7)41(79(44,5)6)16-19-81(8)42(80)15-14-32-33-20-78(3,4)45(119-68(108)31-12-10-11-13-34(31)88)22-83(33,43(90)21-82(32,81)9)77(109)126-76-67(56(101)50(95)38(25-86)117-76)125-73-62(107)64(122-71-60(105)53(98)48(93)36(23-84)114-71)63(30(2)113-73)121-70-59(104)51(96)39(26-87)116-70/h10-14,29-30,33,35-67,69-76,84-107H,15-28H2,1-9H3/t29-,30+,33+,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-,69+,70+,71+,72+,73+,74-,75+,76+,80+,81-,82-,83-/m1/s1
SMILES	OC[C@H]1O[C@@H](OC(=O)[C@@]23C[C@H](OC(=O)c4ccccc4O)C(C[C@H]3C3=CC[C@H]4[C@@]([C@@]3(C[C@H]2O)C)(C)CC[C@@H]2[C@]4(C)CC[C@@H](C2(C)C)O[C@@H]2O[C@H](CO[C@@H]3O[C@H](C)[C@@H]([C@@H]([C@H]3O[C@@H]3OC[C@H]([C@@H]([C@H]3O)O)O)O)O)[C@H]([C@@H]([C@H]2O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@H]([C@@H]([C@H]1O)O)CO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1812.78	Volume:	1686.494 ? Van der Waals volume.
Dense:	1.075	LogP:	-0.348 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.917 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.525 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	25.0	Rigid Bonds:	81.0
TPSA:	676.57 ? Topological Polar Surface Area.	H-Bond Acceptor:	43.0
H-Bond Donor:	24.0	Rings:	14.0
Heavy Atoms:	43.0

MedChem Properties

QED Drug-Likeness Score:	0.027	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.956	Fsp³:	0.88
MCE-18:	409.449 ? 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:	0.682	Fluc inhibitor:	0.322 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.112 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.382	Promiscuous compounds:	0.126

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-8.131	MDCK Permeability:	-4.602
Pgp-inhibitor:	0.0	Pgp-substrate:	0.975
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%):	0.832	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):	58.698%	Volume Distribution (VD):	-0.284
Fu:	22.455% ? 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:	0.13
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):

-2.302

Half-life (T1/2):

6.404

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.427	Drug-induced Liver Injury (DILI):	0.998
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.001	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.21	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.186	RPMI-8226 Immunitoxicity:	0.706
A549 Cytotoxicity:	0.998	Hek293 Cytotoxicity:	0.564
BCF:	0.583 ? 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:	3.378 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.157 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.852 ? 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
NPO7559	Albizia adianthifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662095]
NPO7559	Albizia adianthifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7559	Albizia adianthifolia	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
Activity	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
NPT15	Cell line	Jurkat	Homo sapiens	Activity	=	1.21	n.a.	DrugMatrix in vitro pharmacology data

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 NPC13989 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	17250
0.1-0.2	28596
0.2-0.3	2959
0.3-0.4	642
0.4-0.5	326
0.5-0.6	44
0.6-0.7	22
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8108	Intermediate Similarity	NPC488620
0.7551	Intermediate Similarity	NPC300655
0.7551	Intermediate Similarity	NPC196874
0.7351	Intermediate Similarity	NPC222951
0.7351	Intermediate Similarity	NPC488618
0.7329	Intermediate Similarity	NPC484830
0.7303	Intermediate Similarity	NPC488619
0.7241	Intermediate Similarity	NPC475177
0.7211	Intermediate Similarity	NPC484831
0.7133	Intermediate Similarity	NPC233223
0.7133	Intermediate Similarity	NPC183816
0.7133	Intermediate Similarity	NPC43589
0.7099	Intermediate Similarity	NPC207738
0.7097	Intermediate Similarity	NPC113620
0.7089	Intermediate Similarity	NPC319719
0.7067	Intermediate Similarity	NPC484829
0.7006	Intermediate Similarity	NPC100612
0.6948	Remote Similarity	NPC311178
0.6855	Remote Similarity	NPC322904
0.6842	Remote Similarity	NPC329878
0.6832	Remote Similarity	NPC265699
0.6752	Remote Similarity	NPC475444
0.6752	Remote Similarity	NPC473679
0.6727	Remote Similarity	NPC174336
0.6708	Remote Similarity	NPC324933
0.6688	Remote Similarity	NPC220838
0.6624	Remote Similarity	NPC478559
0.6624	Remote Similarity	NPC478560
0.6601	Remote Similarity	NPC329893
0.6568	Remote Similarity	NPC187497
0.6545	Remote Similarity	NPC488201
0.65	Remote Similarity	NPC482013
0.6306	Remote Similarity	NPC45606
0.6269	Remote Similarity	NPC105800
0.619	Remote Similarity	NPC488202
0.619	Remote Similarity	NPC488204
0.617	Remote Similarity	NPC123522
0.6054	Remote Similarity	NPC470876
0.6028	Remote Similarity	NPC172365
0.5948	Remote Similarity	NPC489209
0.5924	Remote Similarity	NPC489208
0.5878	Remote Similarity	NPC286457
0.5848	Remote Similarity	NPC488203
0.5814	Remote Similarity	NPC488200
0.5753	Remote Similarity	NPC603137
0.5725	Remote Similarity	NPC232237
0.5669	Remote Similarity	NPC33012
0.5664	Remote Similarity	NPC104137
0.5664	Remote Similarity	NPC26626
0.5621	Remote Similarity	NPC309223
0.5605	Remote Similarity	NPC8524
0.5586	Remote Similarity	NPC185466
0.5577	Remote Similarity	NPC102505
0.5577	Remote Similarity	NPC488514
0.5517	Remote Similarity	NPC210729
0.5517	Remote Similarity	NPC82931
0.5461	Remote Similarity	NPC473452
0.5442	Remote Similarity	NPC473824
0.5442	Remote Similarity	NPC610204
0.543	Remote Similarity	NPC85154
0.5417	Remote Similarity	NPC481079
0.535	Remote Similarity	NPC220160
0.535	Remote Similarity	NPC482010
0.5282	Remote Similarity	NPC164389
0.5249	Remote Similarity	NPC488513
0.5235	Remote Similarity	NPC610461
0.5232	Remote Similarity	NPC609305
0.5208	Remote Similarity	NPC123796
0.5203	Remote Similarity	NPC606553
0.5202	Remote Similarity	NPC23020
0.5197	Remote Similarity	NPC283417
0.5197	Remote Similarity	NPC200049
0.5197	Remote Similarity	NPC475140
0.519	Remote Similarity	NPC70809
0.5161	Remote Similarity	NPC13998
0.5135	Remote Similarity	NPC609281
0.5103	Remote Similarity	NPC488517
0.5102	Remote Similarity	NPC606145
0.5072	Remote Similarity	NPC1046
0.507	Remote Similarity	NPC469946
0.5033	Remote Similarity	NPC607904
0.5032	Remote Similarity	NPC4749
0.5031	Remote Similarity	NPC302543

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC13989 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5849
0.1-0.2	3265
0.2-0.3	35
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