NPASS Compound

Natural Product: NPC254202

Natural Product ID	NPC254202
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	12-Epi-19-Deoxyscalarin
IUPAC Name	[(5aS,5bR,7aS,11aS,11bR,13R,13aS,13bR)-5b,8,8,11a,13a-pentamethyl-3-oxo-5,5a,6,7,7a,9,10,11,11b,12,13,13b-dodecahydro-1H-phenanthro[2,1-e][2]benzofuran-13-yl] acetate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL490567
PubChem CID	3012494
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001552] Sesterterpenoids [CHEMONTID:0002883] Scalarane sesterterpenoids

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 71 75 0 0 0 0 0 0 0 0999 V2000 3.7164 4.2611 1.3938 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1109 3.2770 0.4288 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1901 3.4633 -0.8093 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4541 2.1462 0.8784 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8723 1.1959 -0.0217 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3859 1.3918 0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3977 0.2113 -0.3352 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8483 0.4548 -0.4833 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3641 1.5091 0.4551 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0846 1.0752 -1.8776 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5078 1.4680 -2.0150 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5318 0.5285 -1.5260 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1367 -0.5381 -0.5905 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7243 -1.8607 -1.1278 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7484 -0.3563 0.7881 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6493 -0.8009 -0.5253 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2886 -1.8234 0.4866 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8260 -2.1996 0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0067 -0.9454 0.5304 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0272 -0.6976 1.9896 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4169 -1.2907 0.0953 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9366 -2.5589 0.6390 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3756 -2.6919 0.2905 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0553 -1.7780 -0.3422 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4676 -0.4642 -0.8045 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6336 0.4851 -0.7902 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7227 -0.3631 -1.1213 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4377 -1.6954 -0.7639 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3136 -2.5946 -0.8354 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3994 -0.1568 0.2299 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1060 -0.1825 1.5816 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1512 3.7065 2.2671 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9401 4.9263 1.8185 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5066 4.8522 0.9295 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1140 1.5803 -1.0502 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1268 1.6689 1.2012 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1089 2.3076 -0.4350 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0015 -0.0176 -1.3711 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4244 1.7174 0.3291 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8332 2.4655 0.1632 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1533 1.3591 1.5041 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8840 0.2533 -2.6240 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4426 1.9427 -2.0439 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6587 1.7123 -3.1131 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6085 2.4923 -1.5411 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3318 1.1463 -1.0111 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0929 0.1313 -2.4269 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1567 -2.2016 -1.9997 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7657 -1.5794 -1.4554 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8256 -2.6015 -0.3203 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4588 0.5230 0.7596 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0189 -0.2312 1.5856 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4012 -1.2126 1.0901 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4055 -1.2917 -1.5214 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8599 -2.7605 0.2191 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5245 -1.6109 1.5166 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4867 -2.9823 0.9305 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7274 -2.4314 -0.8166 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3294 -1.6490 2.4853 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0377 -0.5495 2.4110 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6072 0.0917 2.3811 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2948 -1.4568 -1.0235 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4262 -3.4097 0.1002 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8289 -2.7642 1.6937 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8707 -3.6066 0.5872 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0206 -0.5662 -1.8135 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5320 1.2204 -1.6103 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8215 0.9860 0.1538 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0385 0.7917 2.1087 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1932 -0.4034 1.4947 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7193 -1.0179 2.2300 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 1 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 13 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 1 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 2 0 25 30 1 0 30 31 1 1 30 5 1 0 19 7 1 0 30 21 1 0 16 8 1 0 28 24 1 0 1 32 1 0 1 33 1 0 1 34 1 0 5 35 1 6 6 36 1 0 6 37 1 0 7 38 1 6 9 39 1 0 9 40 1 0 9 41 1 0 10 42 1 0 10 43 1 0 11 44 1 0 11 45 1 0 12 46 1 0 12 47 1 0 14 48 1 0 14 49 1 0 14 50 1 0 15 51 1 0 15 52 1 0 15 53 1 0 16 54 1 6 17 55 1 0 17 56 1 0 18 57 1 0 18 58 1 0 20 59 1 0 20 60 1 0 20 61 1 0 21 62 1 6 22 63 1 0 22 64 1 0 23 65 1 0 25 66 1 6 26 67 1 0 26 68 1 0 31 69 1 0 31 70 1 0 31 71 1 0 M END

Standard InCHIKey	BTGJLMDMCKFWNM-MGHNXQGFSA-N
Standard InCHI	InChI=1S/C27H40O4/c1-16(28)31-22-14-21-25(4)12-7-11-24(2,3)19(25)10-13-26(21,5)20-9-8-17-18(27(20,22)6)15-30-23(17)29/h8,18-22H,7,9-15H2,1-6H3/t18-,19-,20-,21+,22+,25-,26-,27+/m0/s1
SMILES	CC(=O)O[C@@H]1C[C@@H]2[C@@]3(C)CCCC(C)(C)[C@@H]3CC[C@@]2(C)[C@@H]2CC=C3[C@H](COC3=O)[C@@]12C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	428.29	Volume:	460.017 ? Van der Waals volume.
Dense:	0.931	LogP:	4.462 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.006 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.48 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	27.0
TPSA:	52.6 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	0.0	Rings:	5.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.503	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.809	Fsp³:	0.852
MCE-18:	93.8 ? 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:	0.492	Fluc inhibitor:	0.005 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? 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:	0.468	Promiscuous compounds:	0.305

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.029	MDCK Permeability:	-4.929
Pgp-inhibitor:	0.999	Pgp-substrate:	0.001
PAMPA:	0.339 ? 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%):	0.069	30% Bioavailability (F30%):	0.098
50% Bioavailability (F50%):	0.279

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.107	MRP1:	0.631
Plasma Protein Binding (PPB):	98.496%	Volume Distribution (VD):	0.034
Fu:	2.374% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.93	BCRP inhibitor:	0.065
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.039	CYP1A2-substrate:	0.072
CYP2C19-inhibitor:	0.931	CYP2C19-substrate:	0.562
CYP2C9-inhibitor:	0.11	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.788
CYP3A4-inhibitor:	0.998	CYP3A4-substrate:	0.56
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.112
HLM stability:	0.633 ? 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):

5.252

Half-life (T1/2):

0.691

ADMET: Toxicity

hERG Blockers:	0.016	hERG Blockers (10um):	0.091
Human Hepatotoxicity (H-HT):	0.763	Drug-induced Liver Injury (DILI):	0.94
AMES Toxicity:	0.853	Rat Oral Acute Toxicity:	0.328
Maximum Recommended Daily Dose:	0.646	Skin Sensitization:	0.999
Carcinogencity:	0.977	Eye Corrosion:	0.803
Eye Irritation:	0.915	Respiratory Toxicity:	0.869
Drug-induced Neurotoxicity:	0.076	Ototoxicity:	0.313
Hematotoxicity:	0.906	Drug-induced Nephrotoxicity:	0.984
Genotoxicity:	0.928	RPMI-8226 Immunitoxicity:	0.083
A549 Cytotoxicity:	0.457	Hek293 Cytotoxicity:	0.327
BCF:	1.705 ? 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:	4.345 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.872 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.369 ? 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
NPO33331	brachiaster sp.	Species	n.a.	n.a.	n.a.	Thai	n.a.	PMID[15497961]

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	4
MIC	1

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
NPT83	Cell line	MCF7	Homo sapiens	MIC	=	5210.0	nM	PMID[23869482]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	2340.0	nM	PMID[23869482]
NPT165	Cell line	HeLa	Homo sapiens	IC50	=	5490.0	nM	PMID[23869482]
NPT91	Cell line	KB	Homo sapiens	IC50	=	3010.0	nM	PMID[23869482]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	IC50	=	117000.0	nM	PMID[23869482]

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 NPC254202 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	22155
0.1-0.2	23373
0.2-0.3	3949
0.3-0.4	293
0.4-0.5	63
0.5-0.6	11
0.6-0.7	10
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
0.7091	Intermediate Similarity	NPC605274
0.6885	Remote Similarity	NPC194951
0.6562	Remote Similarity	NPC112457
0.6393	Remote Similarity	NPC269729
0.6393	Remote Similarity	NPC606340
0.6349	Remote Similarity	NPC110496
0.6308	Remote Similarity	NPC228251
0.6308	Remote Similarity	NPC477972
0.6182	Remote Similarity	NPC22611
0.6061	Remote Similarity	NPC94905
0.6061	Remote Similarity	NPC8954
0.5714	Remote Similarity	NPC328141
0.5714	Remote Similarity	NPC602574
0.5522	Remote Similarity	NPC606805
0.5522	Remote Similarity	NPC607360
0.5479	Remote Similarity	NPC20113
0.5373	Remote Similarity	NPC274417
0.5342	Remote Similarity	NPC477968
0.5294	Remote Similarity	NPC275539
0.5294	Remote Similarity	NPC189075
0.5143	Remote Similarity	NPC282233
0.5072	Remote Similarity	NPC9714

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC254202 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7158
0.1-0.2	1921
0.2-0.3	71
0.3-0.4	0
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