NPASS Compound

Natural Product: NPC209342

Natural Product ID	NPC209342
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZHOLUHXKCIXGSR-SQXVBZLISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003568] Androstane steroids [CHEMONTID:0001467] Androgens and derivatives

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 46 49 0 0 0 0 0 0 0 0999 V2000 -2.3946 -1.5584 -1.4571 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9242 -0.7365 -0.2324 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6440 -1.3541 0.9033 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6041 -0.7302 1.5653 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0206 0.6270 1.2142 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9356 1.2307 1.8385 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3165 1.2480 0.0965 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3783 0.6313 -0.5459 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6694 1.3096 -1.6757 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2565 1.4964 -1.0938 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3262 0.1029 -1.0187 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8081 0.1250 -0.7622 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4683 1.4251 -1.1810 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7619 1.4557 -0.3325 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1438 1.1148 0.9786 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3464 1.6330 2.0710 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2146 -0.0076 0.6660 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0251 -1.2624 0.9311 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0868 0.0741 1.6429 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0184 -0.8959 1.2831 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4289 -0.8533 -0.1539 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5104 -2.1709 1.5942 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3267 -1.1380 -1.8732 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5938 -2.6000 -1.1617 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6142 -1.4971 -2.2418 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3966 -2.3527 1.2263 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0945 -1.2377 2.3888 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5843 2.2691 -0.2157 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0931 2.2992 -1.8934 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6180 0.6444 -2.5384 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2755 2.0382 -0.1569 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2561 2.0628 -1.9230 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2281 -0.2480 -2.0743 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3459 -0.6700 -1.3237 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7129 1.4704 -2.2470 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9175 2.3219 -0.8027 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1685 2.4800 -0.3299 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4646 0.6837 -0.6659 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1175 -1.0844 0.8811 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7224 -2.0187 0.1497 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8076 -1.7189 1.9022 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7919 1.1070 1.7730 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5031 -0.2631 2.6373 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8893 -0.8072 1.9325 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2072 -1.8978 -0.5417 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5199 -2.7470 0.7668 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 5 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 15 17 1 0 17 18 1 6 17 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 8 2 1 0 21 11 1 0 21 2 1 0 17 12 1 0 1 23 1 0 1 24 1 0 1 25 1 0 3 26 1 0 4 27 1 0 7 28 1 0 9 29 1 0 9 30 1 0 10 31 1 0 10 32 1 0 11 33 1 6 12 34 1 6 13 35 1 0 13 36 1 0 14 37 1 0 14 38 1 0 18 39 1 0 18 40 1 0 18 41 1 0 19 42 1 0 19 43 1 0 20 44 1 1 21 45 1 6 22 46 1 0 M END

Standard InCHIKey	ZHOLUHXKCIXGSR-SQXVBZLISA-N
Standard InCHI	InChI=1S/C19H24O3/c1-18-8-7-12(20)9-11(18)3-4-13-14-5-6-16(22)19(14,2)10-15(21)17(13)18/h7-9,13-15,17,21H,3-6,10H2,1-2H3/t13-,14+,15-,17-,18-,19-/m0/s1
SMILES	C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]3CCC(=O)[C@@]3(C)C[C@@H]([C@@H]21)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	300.17	Volume:	318.779 ? Van der Waals volume.
Dense:	0.942	LogP:	1.554 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.934 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.732 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	22.0
TPSA:	54.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	4.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.748	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.191	Fsp³:	0.684
MCE-18:	67.188 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.751	Fluc inhibitor:	0.035 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.381 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.455	Promiscuous compounds:	0.584

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.874	MDCK Permeability:	-4.632
Pgp-inhibitor:	0.785	Pgp-substrate:	0.0
PAMPA:	0.274 ? 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%):	0.307	30% Bioavailability (F30%):	0.126
50% Bioavailability (F50%):	0.66

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.334	MRP1:	0.839
Plasma Protein Binding (PPB):	91.631%	Volume Distribution (VD):	0.58
Fu:	9.666% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.905
OATP1B3 inhibitor:	0.94	BCRP inhibitor:	0.0
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.457	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.013	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.28
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.316
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.945
HLM stability:	0.151 ? 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):

10.869

Half-life (T1/2):

1.491

ADMET: Toxicity

hERG Blockers:	0.098	hERG Blockers (10um):	0.384
Human Hepatotoxicity (H-HT):	0.558	Drug-induced Liver Injury (DILI):	0.124
AMES Toxicity:	0.32	Rat Oral Acute Toxicity:	0.776
Maximum Recommended Daily Dose:	0.952	Skin Sensitization:	0.716
Carcinogencity:	0.818	Eye Corrosion:	0.062
Eye Irritation:	0.945	Respiratory Toxicity:	0.857
Drug-induced Neurotoxicity:	0.611	Ototoxicity:	0.382
Hematotoxicity:	0.218	Drug-induced Nephrotoxicity:	0.36
Genotoxicity:	0.966	RPMI-8226 Immunitoxicity:	0.122
A549 Cytotoxicity:	0.018	Hek293 Cytotoxicity:	0.358
BCF:	0.578 ? 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:	3.17 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.463 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.921 ? 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
NPO27960	Dioscorea polygonoides	Species	Dioscoreaceae	Eukaryota	tubers	n.a.	n.a.	PMID[16038563]
NPO27960	Dioscorea polygonoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28674	Prunus verecunda	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18026	Bipolaris sacchari	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28674	Prunus verecunda	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28674	Prunus verecunda	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18026	Bipolaris sacchari	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2459	Verbesina acmella	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27960	Dioscorea polygonoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3952	Paracyclea ochiaiana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO28674	Prunus verecunda	Species	Rosaceae	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

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

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 NPC209342 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	20273
0.1-0.2	27612
0.2-0.3	1885
0.3-0.4	65
0.4-0.5	18
0.5-0.6	2
0.6-0.7	4
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	Natural Product ID
0.6538	Remote Similarity	NPC54123
0.6481	Remote Similarity	NPC257176
0.6102	Remote Similarity	NPC334061
0.6	Remote Similarity	NPC169375
0.5873	Remote Similarity	NPC44063
0.5085	Remote Similarity	NPC6434

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC209342 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7136
0.1-0.2	1772
0.2-0.3	129
0.3-0.4	80
0.4-0.5	17
0.5-0.6	12
0.6-0.7	4
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
0.6491	Remote Similarity	NPD6079	Phase 4
0.6481	Remote Similarity	NPD3618	Phase 1
0.6102	Remote Similarity	NPD4696	Phase 4
0.6	Remote Similarity	NPD5211	Phase 2
0.5873	Remote Similarity	NPD5697	Phase 4
0.5692	Remote Similarity	NPD4729	Approved
0.5692	Remote Similarity	NPD6899	Phase 4
0.5606	Remote Similarity	NPD4730	Phase 4
0.5538	Remote Similarity	NPD4632	Approved
0.5294	Remote Similarity	NPD6054	Phase 4
0.5286	Remote Similarity	NPD6882	Phase 4
0.5217	Remote Similarity	NPD5983	Phase 2
0.5211	Remote Similarity	NPD6333	Approved
0.5211	Remote Similarity	NPD6334	Phase 4
0.5135	Remote Similarity	NPD8297	Phase 4
0.507	Remote Similarity	NPD6370	Phase 4

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