NPASS Compound

Natural Product: NPC51499

Natural Product ID	NPC51499
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	16-Epi-Scalarolbutenolide
IUPAC Name	[(4S,5aS,5bR,7aS,11aS,11bR,13R,13aR,13bS)-13-hydroxy-5b,8,8,11a,13a-pentamethyl-2-oxo-5,5a,6,7,7a,9,10,11,11b,12,13,13b-dodecahydro-4H-phenanthro[1,2-g][1]benzofuran-4-yl] acetate
Synonyms	16-Epi-Scalarolbutenolide
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL476919
PubChem CID	21600071
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 72 76 0 0 0 0 0 0 0 0999 V2000 -5.6938 4.1304 0.8163 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6657 3.2986 0.1528 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9004 3.7755 -0.7372 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4736 1.9434 0.4623 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4952 1.1967 -0.1854 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4194 0.6805 0.7872 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4248 -0.0600 -0.0258 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9442 -1.3472 -0.5838 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0617 -0.9079 -1.5448 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0092 -0.0145 -0.8618 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2177 -0.4929 -1.0051 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1261 -1.7246 -1.7641 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0810 -2.4538 -2.0925 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 -1.9575 -2.0644 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5273 -2.2975 0.3805 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9321 -2.0658 -1.4220 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4311 -3.2734 -1.8595 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3794 -2.2547 -0.6423 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8382 -0.8709 -0.3033 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0651 -0.2003 0.6645 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2513 -0.8924 1.9662 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3863 1.2157 0.9449 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8513 1.3934 1.0335 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6192 0.6904 -0.0481 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3110 -0.7798 0.0269 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6973 -1.4298 1.3024 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0308 -1.5453 -1.0945 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5209 -1.2032 -1.1103 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7180 0.2665 -1.2121 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0509 1.0371 -0.0991 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1577 2.5150 -0.5037 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8098 0.8749 1.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6762 3.6377 0.8975 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3280 4.5456 1.7847 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8471 5.0340 0.1616 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9123 1.7900 -0.9464 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9863 1.5363 1.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9685 0.0804 1.5309 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2001 0.5927 -0.9245 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5368 -0.3015 -2.3175 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1630 -0.0463 -0.6189 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4968 -2.7265 -0.0129 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7411 -1.9386 1.3782 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8777 -3.2144 0.5027 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6745 -1.4386 -2.2964 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8084 -3.6858 -2.5046 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2340 -2.9080 0.2240 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0589 -2.7544 -1.3401 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7394 -0.2848 -1.2704 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5546 -0.6530 2.7212 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4070 -1.9668 1.9275 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1816 -0.4582 2.4410 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0492 1.5185 1.9429 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0606 1.9378 0.2190 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0621 2.4962 0.8939 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1869 1.1653 2.0522 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1645 1.0481 -1.0221 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8815 -0.7474 2.1486 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9477 -2.2326 1.5671 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6617 -2.0124 1.1921 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0083 -2.6299 -0.7742 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5758 -1.3779 -2.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9171 -1.6692 -2.0376 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0491 -1.6753 -0.2645 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4240 0.6059 -2.2142 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8177 0.4685 -1.1150 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8999 3.1819 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1908 2.6498 -0.8848 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4892 2.6269 -1.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7351 1.5179 1.0860 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1884 -0.1612 1.2295 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2779 1.2026 2.0683 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 8 15 1 1 8 16 1 0 16 17 1 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 1 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 10 5 1 0 25 19 1 0 20 7 1 0 30 24 1 0 14 9 1 0 1 33 1 0 1 34 1 0 1 35 1 0 5 36 1 6 6 37 1 0 6 38 1 0 7 39 1 6 9 40 1 6 11 41 1 0 15 42 1 0 15 43 1 0 15 44 1 0 16 45 1 6 17 46 1 0 18 47 1 0 18 48 1 0 19 49 1 6 21 50 1 0 21 51 1 0 21 52 1 0 22 53 1 0 22 54 1 0 23 55 1 0 23 56 1 0 24 57 1 6 26 58 1 0 26 59 1 0 26 60 1 0 27 61 1 0 27 62 1 0 28 63 1 0 28 64 1 0 29 65 1 0 29 66 1 0 31 67 1 0 31 68 1 0 31 69 1 0 32 70 1 0 32 71 1 0 32 72 1 0 M END

Standard InCHIKey	NUXDYAGOJZSDBF-ZWRXBZFVSA-N
Standard InCHI	InChI=1S/C27H40O5/c1-15(28)31-17-13-20-26(5)11-8-18-24(2,3)9-7-10-25(18,4)19(26)14-21(29)27(20,6)23-16(17)12-22(30)32-23/h12,17-21,23,29H,7-11,13-14H2,1-6H3/t17-,18-,19+,20-,21+,23-,25-,26+,27+/m0/s1
SMILES	CC(=O)O[C@H]1C[C@@H]2[C@]([C@@H]3C1=CC(=O)O3)(C)[C@H](O)C[C@H]1[C@@]2(C)CC[C@@H]2[C@]1(C)CCCC2(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	444.29	Volume:	468.808 ? Van der Waals volume.
Dense:	0.948	LogP:	3.41 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.297 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.332 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	27.0
TPSA:	72.83 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	1.0	Rings:	5.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.588	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.996	Fsp³:	0.852
MCE-18:	96.48 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.475	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.018 ? 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:	0.212	Promiscuous compounds:	0.399

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.923	MDCK Permeability:	-4.735
Pgp-inhibitor:	0.962	Pgp-substrate:	0.046
PAMPA:	0.121 ? 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):	0.023
20% Bioavailability (F20%):	0.25	30% Bioavailability (F30%):	0.608
50% Bioavailability (F50%):	0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.323	MRP1:	0.646
Plasma Protein Binding (PPB):	93.471%	Volume Distribution (VD):	-0.297
Fu:	5.741% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.995	BCRP inhibitor:	0.537
BSEP inhibitor:	0.99

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.011
CYP2C19-inhibitor:	0.919	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.28
CYP2D6-inhibitor:	0.455	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.004	CYP2C8-inhibitor:	0.997
HLM stability:	0.825 ? 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):

8.181

Half-life (T1/2):

1.404

ADMET: Toxicity

hERG Blockers:	0.097	hERG Blockers (10um):	0.46
Human Hepatotoxicity (H-HT):	0.676	Drug-induced Liver Injury (DILI):	0.477
AMES Toxicity:	0.404	Rat Oral Acute Toxicity:	0.475
Maximum Recommended Daily Dose:	0.967	Skin Sensitization:	0.982
Carcinogencity:	0.921	Eye Corrosion:	0.004
Eye Irritation:	0.333	Respiratory Toxicity:	0.746
Drug-induced Neurotoxicity:	0.281	Ototoxicity:	0.361
Hematotoxicity:	0.309	Drug-induced Nephrotoxicity:	0.763
Genotoxicity:	0.549	RPMI-8226 Immunitoxicity:	0.133
A549 Cytotoxicity:	0.109	Hek293 Cytotoxicity:	0.5
BCF:	1.317 ? 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:	4.406 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.093 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.579 ? 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
NPO33333	hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[11809054]
NPO33333	hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Indian Ocean	n.a.	PMID[16124771]
NPO33333	hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[16378375]
NPO25507	Spongia agaricina	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548857]
NPO33333	hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9584401]
NPO33333	hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Maldives	n.a.	PMID[9873492]
NPO25507	Spongia agaricina	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25507	Spongia agaricina	Species	Spongiidae	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
Inhibition	1
IC50	4

Activity Type	# Activity
Cell line	4
Organism	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
NPT168	Cell line	P388	Mus musculus	IC50	=	5.0	ug.mL-1	PMID[9722490]
NPT81	Cell line	A549	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[19029333]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[19029333]
NPT170	Cell line	SK-MEL-28	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[19029333]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	Inhibition	=	40.0	%	PMID[19307369]

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 NPC51499 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	16740
0.1-0.2	25530
0.2-0.3	7056
0.3-0.4	459
0.4-0.5	64
0.5-0.6	7
0.6-0.7	1
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
0.6833	Remote Similarity	NPC275086
0.5758	Remote Similarity	NPC325229
0.5672	Remote Similarity	NPC165250
0.5672	Remote Similarity	NPC604992
0.5352	Remote Similarity	NPC97867
0.5224	Remote Similarity	NPC95899
0.5079	Remote Similarity	NPC206060
0.5075	Remote Similarity	NPC12046

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC51499 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6576
0.1-0.2	2452
0.2-0.3	121
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