NPASS Compound

Natural Product: NPC252469

Natural Product ID	NPC252469
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WPGPCDVQHXOMQP-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	521267
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0001401] Menthane monoterpenoids

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 27 27 0 0 0 0 0 0 0 0999 V2000 -2.4302 -1.0747 -1.1987 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8964 -0.3549 -0.0068 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7366 0.8779 0.2315 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4336 -0.0073 -0.1434 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0390 0.7185 1.0973 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4757 1.0646 0.9320 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3124 0.3208 0.2392 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7464 0.6601 0.0704 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8271 -0.9129 -0.4098 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6433 -1.6320 -1.0422 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3853 -1.2522 -0.2858 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4874 -1.3396 -0.9956 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4441 -0.3791 -2.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9048 -2.0226 -1.4192 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9781 -1.0402 0.8709 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2220 1.7950 -0.1434 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0421 0.9880 1.2949 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7077 0.8260 -0.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2469 0.6663 -1.0005 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0634 0.1010 2.0113 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5454 1.6428 1.2517 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9034 1.9670 1.3873 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3404 -0.2637 0.2932 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9717 0.9170 -0.9898 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0876 1.4245 0.7843 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2919 -1.8111 0.6887 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1147 -1.8794 -1.1426 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 2 0 9 11 1 0 11 4 1 0 1 12 1 0 1 13 1 0 1 14 1 0 2 15 1 0 3 16 1 0 3 17 1 0 3 18 1 0 4 19 1 0 5 20 1 0 5 21 1 0 6 22 1 0 8 23 1 0 8 24 1 0 8 25 1 0 11 26 1 0 11 27 1 0 M END

Standard InCHIKey	WPGPCDVQHXOMQP-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H16O/c1-7(2)9-5-4-8(3)10(11)6-9/h4,7,9H,5-6H2,1-3H3
SMILES	CC(C)C1CC=C(C)C(=O)C1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	152.12	Volume:	176.477 ? Van der Waals volume.
Dense:	0.862	LogP:	2.83 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.695 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.206 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	7.0
TPSA:	17.07 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.564	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.247	Fsp³:	0.7
MCE-18:	16.471 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.219	Fluc inhibitor:	0.02 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.008 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.013 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.996	Promiscuous compounds:	0.028

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.864	MDCK Permeability:	-4.543
Pgp-inhibitor:	0.972	Pgp-substrate:	0.017
PAMPA:	0.074 ? 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%):	0.049	30% Bioavailability (F30%):	0.211
50% Bioavailability (F50%):	0.744

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052	MRP1:	0.954
Plasma Protein Binding (PPB):	41.313%	Volume Distribution (VD):	0.207
Fu:	59.038% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.993
OATP1B3 inhibitor:	0.988	BCRP inhibitor:	0.088
BSEP inhibitor:	0.987

ADMET: Metabolism

CYP1A2-inhibitor:	0.041	CYP1A2-substrate:	0.983
CYP2C19-inhibitor:	0.918	CYP2C19-substrate:	0.767
CYP2C9-inhibitor:	0.704	CYP2C9-substrate:	0.098
CYP2D6-inhibitor:	0.164	CYP2D6-substrate:	0.606
CYP3A4-inhibitor:	0.364	CYP3A4-substrate:	0.285
CYP2B6-substrate:	0.539	CYP2C8-inhibitor:	0.678
HLM stability:	0.975 ? 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):

9.34

Half-life (T1/2):

0.888

ADMET: Toxicity

hERG Blockers:	0.116	hERG Blockers (10um):	0.515
Human Hepatotoxicity (H-HT):	0.635	Drug-induced Liver Injury (DILI):	0.388
AMES Toxicity:	0.401	Rat Oral Acute Toxicity:	0.274
Maximum Recommended Daily Dose:	0.373	Skin Sensitization:	0.784
Carcinogencity:	0.629	Eye Corrosion:	0.967
Eye Irritation:	0.989	Respiratory Toxicity:	0.705
Drug-induced Neurotoxicity:	0.58	Ototoxicity:	0.348
Hematotoxicity:	0.373	Drug-induced Nephrotoxicity:	0.29
Genotoxicity:	0.04	RPMI-8226 Immunitoxicity:	0.068
A549 Cytotoxicity:	0.123	Hek293 Cytotoxicity:	0.189
BCF:	1.091 ? 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:	3.504 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.752 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.308 ? 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
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)94055-X]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	flower	n.a.	DOI[10.3390/70200245]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[12088434]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	Roots	n.a.	n.a.	PMID[14510592]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21707257]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24617303]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29726697]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34443694]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34770961]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[35631245]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572418]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36840093]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37020229]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37226152]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38257205]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38370080]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38381096]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38695450]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39407547]
NPO55878	Origanum vulgare L. ssp. hirtum	Genus	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39407547]
NPO50502	Origanum vulgare L. ssp. vulgare	Genus	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39407547]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25825	Saussurea lappa	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
NPO19472	Thymus vulgaris	Oil	n.a.	2.77	n.a.	n.a.	%	PMID[39407547]
NPO50502	Origanum vulgare L. ssp. vulgare	Oil	n.a.	0.25	n.a.	n.a.	%	PMID[39407547]
NPO55878	Origanum vulgare L. ssp. hirtum	Oil	n.a.	0.13	n.a.	n.a.	%	PMID[39407547]

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 NPC252469 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	22679
0.1-0.2	25713
0.2-0.3	1391
0.3-0.4	66
0.4-0.5	6
0.5-0.6	4
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	Natural Product ID
0.5926	Remote Similarity	NPC58970
0.5926	Remote Similarity	NPC176819
0.5926	Remote Similarity	NPC163984
0.5517	Remote Similarity	NPC602120

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC252469 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6791
0.1-0.2	2288
0.2-0.3	70
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