NPASS Compound

Natural Product: NPC475531

Natural Product ID	NPC475531
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	[(3S,8S,9R,10R,12R,13R,14R,17S)-8,14,17-Trihydroxy-3-[(2R,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,3R,4R,5R,6R)-3-Hydroxy-4-Methoxy-6-Methyl-5-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyoxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-4-Methoxy-6-Methyloxan-2-Yl]Oxy-10,13-Dimethyl-17-[(1S)-1-[(E)-3-Phenylprop-2-Enoyl]Oxyethyl]-1,2,3,4,7,9,11,12,15,16-Decahydrocyclopenta[A]Phenanthren-12-Yl] Benzoate
IUPAC Name	[(3S,8S,9R,10R,12R,13R,14R,17S)-8,14,17-trihydroxy-3-[(2R,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,4S,5R,6R)-5-[(2S,3R,4R,5R,6R)-3-hydroxy-4-methoxy-6-methyl-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-4-methoxy-6-methyloxan-2-yl]oxy-10,13-dimethyl-17-[(1S)-1-[(E)-3-phenylprop-2-enoyl]oxyethyl]-1,2,3,4,7,9,11,12,15,16-decahydrocyclopenta[a]phenanthren-12-yl] benzoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL507437
PubChem CID	44566876
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

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 199209 0 0 0 0 0 0 0 0999 V2000 0.1363 -1.8984 -2.5874 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0260 -0.9106 -1.8453 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1417 0.0878 -1.1630 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0370 1.1305 -0.5199 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7900 1.7930 -1.6466 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5766 0.7180 -2.3575 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7386 -0.2417 -2.8516 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4146 0.1042 -1.4227 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7514 0.2801 -1.7343 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3890 -1.0148 -2.2415 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8069 -0.7046 -2.7021 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6062 -0.0905 -1.5603 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9301 -0.7821 -1.3271 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9440 0.2008 -0.8355 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1974 -0.4124 -0.2206 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3736 -1.8530 -0.6930 C 0 0 0 0 0 0 0 0 0 0 0 0 12.4316 -2.6162 0.0628 C 0 0 0 0 0 0 0 0 0 0 0 0 11.9117 -4.0151 0.1333 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4781 -3.9742 -0.4743 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1335 -2.5597 -0.1600 C 0 0 0 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23 1 0 23 24 2 0 24 25 1 0 21 26 1 0 20 27 1 0 17 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 33 34 2 3 34 35 1 0 35 36 2 0 36 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 17 41 1 0 16 42 1 0 15 43 1 0 43 44 1 0 44 45 2 0 44 46 1 0 46 47 2 0 47 48 1 0 48 49 2 0 49 50 1 0 50 51 2 0 12 52 1 0 4 53 1 0 53 54 1 0 3 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 60 61 1 0 60 62 1 0 59 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 68 69 1 0 68 70 1 0 67 71 1 0 71 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 75 76 1 0 76 77 1 0 76 78 1 0 75 79 1 0 79 80 1 0 80 81 1 0 81 82 1 0 82 83 1 0 83 84 1 0 84 85 1 0 84 86 1 0 86 87 1 0 83 88 1 0 82 89 1 0 81 90 1 0 74 91 1 0 91 92 1 0 73 93 1 0 66 94 1 0 94 95 1 0 58 96 1 0 96 97 1 0 7 2 1 0 77 72 1 0 85 80 1 0 25 9 1 0 24 12 1 0 21 13 1 0 20 16 1 0 40 35 1 0 51 46 1 0 61 56 1 0 69 64 1 0 1 98 1 0 1 99 1 0 1100 1 0 2101 1 0 3102 1 0 4103 1 0 5104 1 0 5105 1 0 6106 1 0 9107 1 0 10108 1 0 10109 1 0 11110 1 0 11111 1 0 13112 1 0 14113 1 0 14114 1 0 15115 1 0 18116 1 0 18117 1 0 19118 1 0 19119 1 0 22120 1 0 22121 1 0 23122 1 0 25123 1 0 25124 1 0 26125 1 0 27126 1 0 28127 1 0 29128 1 0 29129 1 0 29130 1 0 33131 1 0 34132 1 0 36133 1 0 37134 1 0 38135 1 0 39136 1 0 40137 1 0 41138 1 0 42139 1 0 42140 1 0 42141 1 0 47142 1 0 48143 1 0 49144 1 0 50145 1 0 51146 1 0 52147 1 0 52148 1 0 52149 1 0 54150 1 0 54151 1 0 54152 1 0 56153 1 0 57154 1 0 57155 1 0 58156 1 0 59157 1 0 60158 1 0 62159 1 0 62160 1 0 62161 1 0 64162 1 0 65163 1 0 65164 1 0 66165 1 0 67166 1 0 68167 1 0 70168 1 0 70169 1 0 70170 1 0 72171 1 0 73172 1 0 74173 1 0 75174 1 0 76175 1 0 78176 1 0 78177 1 0 78178 1 0 80179 1 0 81180 1 0 82181 1 0 83182 1 0 84183 1 0 86184 1 0 86185 1 0 87186 1 0 88187 1 0 89188 1 0 90189 1 0 92190 1 0 92191 1 0 92192 1 0 93193 1 0 95194 1 0 95195 1 0 95196 1 0 97197 1 0 97198 1 0 97199 1 0 M END

Standard InCHIKey	MDLPSLZTXRUNDJ-RBRNAYMRSA-N
Standard InCHI	InChI=1S/C71H102O26/c1-36-59(94-53-32-46(83-9)60(37(2)87-53)95-54-33-47(84-10)61(38(3)88-54)96-66-58(77)63(85-11)62(39(4)89-66)97-65-57(76)56(75)55(74)48(35-72)92-65)45(82-8)31-52(86-36)91-44-25-26-67(6)43(30-44)24-27-70(80)49(67)34-50(93-64(78)42-20-16-13-17-21-42)68(7)69(79,28-29-71(68,70)81)40(5)90-51(73)23-22-41-18-14-12-15-19-41/h12-24,36-40,44-50,52-63,65-66,72,74-77,79-81H,25-35H2,1-11H3/b23-22+/t36-,37-,38-,39-,40+,44+,45+,46+,47+,48-,49-,50-,52+,53+,54+,55-,56+,57-,58-,59-,60-,61-,62-,63-,65+,66+,67+,68-,69-,70+,71-/m1/s1
SMILES	CC1C(C(CC(O1)OC2CCC3(C4CC(C5(C(CCC5(C4(CC=C3C2)O)O)(C(C)OC(=O)C=CC6=CC=CC=C6)O)C)OC(=O)C7=CC=CC=C7)C)OC)OC8CC(C(C(O8)C)OC9CC(C(C(O9)C)OC1C(C(C(C(O1)C)OC1C(C(C(C(O1)CO)O)O)O)OC)O)OC)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1370.67	Volume:	1344.632 ? Van der Waals volume.
Dense:	1.019	LogP:	3.548 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.382 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.744 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	23.0	Rigid Bonds:	65.0
TPSA:	343.66 ? Topological Polar Surface Area.	H-Bond Acceptor:	26.0
H-Bond Donor:	8.0	Rings:	11.0
Heavy Atoms:	26.0

MedChem Properties

QED Drug-Likeness Score:	0.05	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.634	Fsp³:	0.746
MCE-18:	287.968 ? 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:	0.269	Fluc inhibitor:	0.315 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.042 ? 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:	0.399	Promiscuous compounds:	0.002

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.834	MDCK Permeability:	-5.247
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):	0.97
20% Bioavailability (F20%):	0.374	30% Bioavailability (F30%):	0.984
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	65.39%	Volume Distribution (VD):	-0.555
Fu:	34.686% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.044	BCRP inhibitor:	0.0
BSEP inhibitor:	0.53

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.996	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.905	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.738	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.006	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):

0.879

Half-life (T1/2):

7.08

ADMET: Toxicity

hERG Blockers:	0.322	hERG Blockers (10um):	0.71
Human Hepatotoxicity (H-HT):	0.157	Drug-induced Liver Injury (DILI):	0.89
AMES Toxicity:	0.717	Rat Oral Acute Toxicity:	0.623
Maximum Recommended Daily Dose:	0.702	Skin Sensitization:	0.585
Carcinogencity:	0.007	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.802	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.021
Genotoxicity:	0.374	RPMI-8226 Immunitoxicity:	0.464
A549 Cytotoxicity:	0.346	Hek293 Cytotoxicity:	0.993
BCF:	0.601 ? 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:	3.788 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.946 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.615 ? 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
NPO33108	leptadenia hastata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7623046]
NPO33108	leptadenia hastata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8786361]

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	6

Activity Type	# Activity
Cell line	6

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	13.0	%	PMID[20430633]
NPT80	Cell line	Raji	Homo sapiens	Activity	=	14.0	%	PMID[20430633]
NPT80	Cell line	Raji	Homo sapiens	Activity	=	16.0	%	DrugMatrix in vivo data: Biochemistry
NPT80	Cell line	Raji	Homo sapiens	Activity	=	5.0	%	DrugMatrix in vivo data: Biochemistry
NPT80	Cell line	Raji	Homo sapiens	Activity	=	4.0	%	DrugMatrix in vivo data: Biochemistry

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 NPC475531 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	12653
0.1-0.2	31627
0.2-0.3	5199
0.3-0.4	330
0.4-0.5	13
0.5-0.6	7
0.6-0.7	16
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC475198
0.9292	High Similarity	NPC475175
0.8174	Intermediate Similarity	NPC473641
0.8174	Intermediate Similarity	NPC475300
0.8017	Intermediate Similarity	NPC70236
0.7874	Intermediate Similarity	NPC476090
0.7851	Intermediate Similarity	NPC473797
0.7705	Intermediate Similarity	NPC475447
0.7521	Intermediate Similarity	NPC475567
0.7438	Intermediate Similarity	NPC475437
0.7438	Intermediate Similarity	NPC475464
0.7295	Intermediate Similarity	NPC476092
0.7049	Intermediate Similarity	NPC475218
0.6891	Remote Similarity	NPC473468
0.6885	Remote Similarity	NPC475613
0.6885	Remote Similarity	NPC481654
0.6724	Remote Similarity	NPC102015
0.6587	Remote Similarity	NPC473557
0.6581	Remote Similarity	NPC475358
0.6581	Remote Similarity	NPC473566
0.6504	Remote Similarity	NPC475536
0.6489	Remote Similarity	NPC481660
0.6393	Remote Similarity	NPC165234
0.6393	Remote Similarity	NPC481659
0.6393	Remote Similarity	NPC271687
0.6371	Remote Similarity	NPC474564
0.635	Remote Similarity	NPC481650
0.6033	Remote Similarity	NPC481661
0.6033	Remote Similarity	NPC481655
0.5232	Remote Similarity	NPC481647
0.5227	Remote Similarity	NPC481662
0.5203	Remote Similarity	NPC473519
0.5078	Remote Similarity	NPC473805
0.507	Remote Similarity	NPC481648
0.5041	Remote Similarity	NPC481657
0.5039	Remote Similarity	NPC305378

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC475531 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4939
0.1-0.2	4135
0.2-0.3	73
0.3-0.4	3
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