NPASS Compound

Natural Product: NPC486031

Natural Product ID	NPC486031
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HUSWYTADELXPIC-WGBGBEOUSA-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:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides 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 53 54 0 0 0 0 0 0 0 0999 V2000 -1.5391 -2.7263 -0.1933 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6278 -1.4285 -0.8955 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7725 -0.9892 -1.3237 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1494 -1.5441 -1.2523 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7747 -0.7354 -0.0159 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8618 0.5140 -0.0333 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7873 0.4513 0.7417 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7245 1.4253 0.9425 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3856 0.7420 1.2260 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3498 1.8897 1.7645 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5518 2.3617 1.6702 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6869 2.5663 2.5971 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4170 3.3850 3.5388 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9217 2.1513 2.1675 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2126 -0.1510 0.2781 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3975 -0.5407 -1.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6224 0.0757 0.0808 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5860 -0.7932 0.5026 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2614 -1.8492 1.1240 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0269 -0.5020 0.2311 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3196 0.5659 -0.4375 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6426 1.0678 -0.8240 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6966 1.1353 -2.2377 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0170 -1.4691 0.7287 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3051 -1.1967 0.4505 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2140 1.6077 -0.9434 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0462 -0.4606 -0.2959 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2099 -2.6985 0.6845 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8353 -3.5794 -0.8686 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5032 -2.9522 0.1451 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7268 -0.0065 -1.8713 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7351 -1.2185 -2.1016 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2385 -2.5975 -1.0656 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6014 -1.3640 0.8316 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7095 -0.4719 1.3746 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5976 2.1772 0.1642 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6597 0.1352 2.1868 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3617 1.9580 1.1057 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8584 3.2939 2.2091 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2612 -1.1977 0.8253 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3444 -1.1815 -1.5487 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6072 0.3038 -1.6949 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4381 1.1946 -0.7895 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6791 2.1852 -0.5098 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5186 0.6125 -0.4053 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2978 0.3984 -2.5392 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8797 -1.6101 1.8476 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7877 -2.4756 0.2353 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8649 -2.0211 0.3520 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3345 2.2161 -1.2603 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7554 1.2482 -1.8551 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8631 2.3277 -0.3691 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2000 -0.2295 -1.2547 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 12 14 1 0 9 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 20 24 1 0 24 25 1 0 6 26 1 0 5 27 1 0 16 2 1 0 14 8 1 0 1 28 1 0 1 29 1 0 1 30 1 0 3 31 1 0 4 32 1 0 4 33 1 0 5 34 1 1 7 35 1 0 8 36 1 6 9 37 1 1 11 38 1 0 11 39 1 0 15 40 1 1 16 41 1 0 16 42 1 0 21 43 1 0 22 44 1 0 22 45 1 0 23 46 1 0 24 47 1 0 24 48 1 0 25 49 1 0 26 50 1 0 26 51 1 0 26 52 1 0 27 53 1 0 M END

Standard InCHIKey	HUSWYTADELXPIC-WGBGBEOUSA-N
Standard InCHI	InChI=1S/C20H26O7/c1-11-4-5-15(23)12(2)9-17-18(13(3)19(24)26-17)16(8-11)27-20(25)14(10-22)6-7-21/h4,6,9,15-18,21-23H,3,5,7-8,10H2,1-2H3/b11-4+,12-9+,14-6+/t15-,16+,17+,18+/m0/s1
SMILES	C/C/1=CC[C@@H](/C(=C/[C@@H]2[C@H](C(=C)C(=O)O2)[C@@H](C1)OC(=O)/C(=C/CO)/CO)/C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	378.17	Volume:	383.076 ? Van der Waals volume.
Dense:	0.987	LogP:	1.042 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.479 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.365 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	18.0
TPSA:	113.29 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	3.0	Rings:	2.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.379	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.098	Fsp³:	0.5
MCE-18:	38.4 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.109	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.037 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.039 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.587	Promiscuous compounds:	0.555

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.014	MDCK Permeability:	-4.692
Pgp-inhibitor:	0.05	Pgp-substrate:	0.753
PAMPA:	0.966 ? 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):	0.3
20% Bioavailability (F20%):	0.958	30% Bioavailability (F30%):	0.998
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.783
Plasma Protein Binding (PPB):	62.26%	Volume Distribution (VD):	-0.22
Fu:	34.8% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.998
OATP1B3 inhibitor:	0.992	BCRP inhibitor:	0.004
BSEP inhibitor:	0.817

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.067	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.52
HLM stability:	0.006 ? 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):

8.631

Half-life (T1/2):

1.256

ADMET: Toxicity

hERG Blockers:	0.004	hERG Blockers (10um):	0.028
Human Hepatotoxicity (H-HT):	0.931	Drug-induced Liver Injury (DILI):	0.941
AMES Toxicity:	0.501	Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.357	Skin Sensitization:	0.999
Carcinogencity:	0.747	Eye Corrosion:	0.002
Eye Irritation:	0.76	Respiratory Toxicity:	0.19
Drug-induced Neurotoxicity:	0.135	Ototoxicity:	0.796
Hematotoxicity:	0.665	Drug-induced Nephrotoxicity:	0.947
Genotoxicity:	0.575	RPMI-8226 Immunitoxicity:	0.124
A549 Cytotoxicity:	0.06	Hek293 Cytotoxicity:	0.109
BCF:	0.51 ? 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:	3.24 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.011 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.208 ? 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
NPO2440	Schkuhria pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29244495]
NPO691	Tarchonanthus camphoratus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29244495]
NPO2440	Schkuhria pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO691	Tarchonanthus camphoratus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2440	Schkuhria pinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO691	Tarchonanthus camphoratus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2440	Schkuhria pinnata	Species	Asteraceae	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	2
Ratio IC50	1

Activity Type	# Activity
Cell line	1
Organism	1
Others	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
NPT839	Cell line	L6	Rattus norvegicus	IC50	=	51700.0	nM	PMID[29244495]
NPT844	Organism	Trypanosoma brucei rhodesiense	Trypanosoma brucei rhodesiense	IC50	=	5400.0	nM	PMID[29244495]
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	9.6	n.a.	PMID[29244495]

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 NPC486031 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	17333
0.1-0.2	29033
0.2-0.3	3000
0.3-0.4	381
0.4-0.5	64
0.5-0.6	27
0.6-0.7	9
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
0.8039	Intermediate Similarity	NPC250940
0.8039	Intermediate Similarity	NPC169575
0.7547	Intermediate Similarity	NPC488296
0.7258	Intermediate Similarity	NPC486030
0.7143	Intermediate Similarity	NPC470755
0.7143	Intermediate Similarity	NPC298801
0.7031	Intermediate Similarity	NPC486032
0.678	Remote Similarity	NPC134725
0.678	Remote Similarity	NPC48657
0.6508	Remote Similarity	NPC486033
0.6491	Remote Similarity	NPC488298
0.6379	Remote Similarity	NPC482126
0.619	Remote Similarity	NPC486037
0.6	Remote Similarity	NPC482130
0.6	Remote Similarity	NPC482128
0.6	Remote Similarity	NPC482129
0.5862	Remote Similarity	NPC488302
0.5862	Remote Similarity	NPC475461
0.5862	Remote Similarity	NPC488300
0.5862	Remote Similarity	NPC488301
0.5667	Remote Similarity	NPC158756
0.5667	Remote Similarity	NPC488297
0.5667	Remote Similarity	NPC601035
0.5645	Remote Similarity	NPC482127
0.5645	Remote Similarity	NPC469910
0.5645	Remote Similarity	NPC269509
0.5614	Remote Similarity	NPC471465
0.5574	Remote Similarity	NPC482131
0.5556	Remote Similarity	NPC482133
0.5556	Remote Similarity	NPC482134
0.5538	Remote Similarity	NPC288876
0.5469	Remote Similarity	NPC281005
0.5455	Remote Similarity	NPC482132
0.5362	Remote Similarity	NPC59330
0.5273	Remote Similarity	NPC488299
0.5224	Remote Similarity	NPC96018
0.5172	Remote Similarity	NPC611318
0.5161	Remote Similarity	NPC475838
0.5161	Remote Similarity	NPC488303
0.5161	Remote Similarity	NPC481909
0.5161	Remote Similarity	NPC125674
0.5161	Remote Similarity	NPC228451
0.5082	Remote Similarity	NPC116543

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486031 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6658
0.1-0.2	2465
0.2-0.3	25
0.3-0.4	2
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