NPASS Compound

Natural Product: NPC476961

Natural Product ID	NPC476961
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Withametelin J
IUPAC Name	(1R,5R,8R)-5-methyl-4-methylidene-8-[(5R,6R,12R)-5,6,12-trihydroxy-10,13-dimethyl-1-oxo-6,7,8,9,11,12,14,15,16,17-decahydro-4H-cyclopenta[a]phenanthren-17-yl]-2,6-dioxabicyclo[3.3.1]nonan-3-one
Synonyms	withametelin J
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44425444
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones

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 73 78 0 0 0 0 0 0 0 0999 V2000 5.8653 0.4972 1.6975 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2955 -0.1756 0.4576 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6671 0.8960 -0.4142 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8253 0.1817 -1.4022 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6654 -0.5727 -0.7417 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2839 -1.4102 0.3275 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4820 -1.1678 0.8174 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6714 0.4229 -0.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2480 1.2388 -1.5299 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0106 1.9536 -0.9431 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6628 0.7586 -0.4017 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4499 0.0255 0.3711 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0404 -1.3642 0.4399 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5249 -1.5387 0.1889 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3960 -0.4539 0.7074 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8710 0.9422 0.4310 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8519 1.8385 -0.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2402 1.7917 0.2910 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6167 0.4928 0.9294 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8146 -0.6643 0.3280 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1526 -0.7235 -1.0838 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4088 -0.8145 -2.0698 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5969 -0.6681 -1.4052 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4823 -0.2148 -0.5365 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0956 0.2659 0.8086 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2858 -1.9211 1.0794 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3339 0.5959 2.3061 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1107 2.1197 -0.7744 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5679 -2.2583 -0.4378 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4377 0.6061 1.7758 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6103 -0.8524 -2.0197 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9908 -0.9819 -1.7722 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8151 -1.2803 -2.6613 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3778 -0.7387 -0.3911 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5930 -1.0090 0.0274 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3784 -0.2753 2.3156 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0057 0.8453 2.3066 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5296 1.3420 1.4352 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4857 1.4033 -1.0074 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2026 1.6790 0.1658 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4945 0.8003 -2.2588 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2775 -1.1849 -1.6058 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2725 -2.4772 -0.0566 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5591 -1.4423 1.1912 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2461 1.1798 0.3165 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8610 0.6128 -2.3367 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9664 2.0139 -1.8000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2887 2.7264 -0.2319 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5442 2.3705 -1.8046 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9415 0.1149 -1.2920 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1397 -1.7831 1.4576 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 -1.7565 -0.8859 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8534 -2.4903 0.7046 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3930 -0.5762 1.8361 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6090 1.4660 1.3965 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8156 1.7612 -1.3786 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4863 2.8977 -0.0837 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4119 2.6159 1.0439 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9637 -1.0012 -2.3692 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5485 -0.1787 -0.7857 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6013 1.2711 0.9181 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5072 -0.3750 1.6171 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8188 -1.8720 2.0803 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3714 -1.9907 1.1341 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8597 -2.7872 0.5338 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8975 -0.0352 2.8164 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6329 2.3847 -1.5778 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9154 -3.0624 -0.0131 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3554 1.7130 1.7598 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4891 0.4373 2.1652 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2054 0.0909 2.4791 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3650 -1.4189 -0.6094 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9103 -0.8360 1.0593 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 5 8 1 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 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 2 0 24 25 1 0 20 26 1 0 19 27 1 1 18 28 1 0 13 29 1 0 12 30 1 0 4 31 1 0 31 32 1 0 32 33 2 0 32 34 1 0 34 35 2 0 7 2 1 0 34 2 1 0 12 8 1 0 16 11 1 0 20 15 1 0 25 19 1 0 1 36 1 0 1 37 1 0 1 38 1 0 3 39 1 0 3 40 1 0 4 41 1 6 5 42 1 6 6 43 1 0 6 44 1 0 8 45 1 0 9 46 1 0 9 47 1 0 10 48 1 0 10 49 1 0 11 50 1 0 13 51 1 1 14 52 1 0 14 53 1 0 15 54 1 0 16 55 1 0 17 56 1 0 17 57 1 0 18 58 1 1 23 59 1 0 24 60 1 0 25 61 1 0 25 62 1 0 26 63 1 0 26 64 1 0 26 65 1 0 27 66 1 0 28 67 1 0 29 68 1 0 30 69 1 0 30 70 1 0 30 71 1 0 35 72 1 0 35 73 1 0 M END

Standard InCHIKey	NUGSWDUYOFBMPP-RNFOTZJJSA-N
Standard InCHI	InChI=1S/C28H38O7/c1-14-24(32)35-20-12-25(14,2)34-13-16(20)18-8-7-17-15-10-23(31)28(33)9-5-6-21(29)27(28,4)19(15)11-22(30)26(17,18)3/h5-6,15-20,22-23,30-31,33H,1,7-13H2,2-4H3/t15?,16-,17?,18?,19?,20+,22+,23+,25+,26?,27?,28-/m0/s1
SMILES	C[C@]12C[C@H]([C@@H](CO1)C3CCC4C3([C@@H](CC5C4C[C@H]([C@@]6(C5(C(=O)C=CC6)C)O)O)O)C)OC(=O)C2=C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	486.26	Volume:	492.491 ? Van der Waals volume.
Dense:	0.987	LogP:	2.054 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.531 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.871 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	33.0
TPSA:	113.29 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.385	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.244	Fsp³:	0.786
MCE-18:	113.16 ? 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:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.346	Fluc inhibitor:	0.011 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.015 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.042 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.151	Promiscuous compounds:	0.32

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.066	MDCK Permeability:	-4.806
Pgp-inhibitor:	0.068	Pgp-substrate:	0.266
PAMPA:	0.893 ? 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):	0.0
20% Bioavailability (F20%):	0.154	30% Bioavailability (F30%):	0.594
50% Bioavailability (F50%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.4
Plasma Protein Binding (PPB):	91.279%	Volume Distribution (VD):	0.177
Fu:	9.128% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.061
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.003	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.015	CYP3A4-substrate:	0.003
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.713
HLM stability:	0.026 ? 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):

10.749

Half-life (T1/2):

3.077

ADMET: Toxicity

hERG Blockers:	0.017	hERG Blockers (10um):	0.079
Human Hepatotoxicity (H-HT):	0.823	Drug-induced Liver Injury (DILI):	0.182
AMES Toxicity:	0.661	Rat Oral Acute Toxicity:	0.48
Maximum Recommended Daily Dose:	0.968	Skin Sensitization:	0.992
Carcinogencity:	0.755	Eye Corrosion:	0.0
Eye Irritation:	0.082	Respiratory Toxicity:	0.103
Drug-induced Neurotoxicity:	0.119	Ototoxicity:	0.888
Hematotoxicity:	0.279	Drug-induced Nephrotoxicity:	0.895
Genotoxicity:	0.981	RPMI-8226 Immunitoxicity:	0.395
A549 Cytotoxicity:	0.046	Hek293 Cytotoxicity:	0.418
BCF:	0.629 ? 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:	3.472 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.185 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.292 ? 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
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.3906/biy-1405-25]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	flowers	Yuxi Town, Fuqing City, Fujian Province, China	2005-SEP	PMID[17583953]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24850	Datura metel	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24850	Datura metel	Species	Solanaceae	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	3

Activity Type	# Activity
Cell line	3

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
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000	nM	PMID[17583953]
NPT547	Cell line	BGC-823	Homo sapiens	IC50	=	5200	nM	PMID[17583953]
NPT111	Cell line	K562	Homo sapiens	IC50	=	2500	nM	PMID[17583953]

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 NPC476961 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	15181
0.1-0.2	30955
0.2-0.3	3632
0.3-0.4	55
0.4-0.5	27
0.5-0.6	3
0.6-0.7	3
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8082	Intermediate Similarity	NPC470959
0.8082	Intermediate Similarity	NPC476965
0.6543	Remote Similarity	NPC470953
0.65	Remote Similarity	NPC476962
0.6386	Remote Similarity	NPC476960
0.5952	Remote Similarity	NPC476963
0.5581	Remote Similarity	NPC476959
0.5366	Remote Similarity	NPC147912

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC476961 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5660
0.1-0.2	3342
0.2-0.3	147
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