Natural Product: NPC134291

Natural Product IDNPC134291
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OZBFUQLOVFXDNK-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 118088
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001564] Bicyclic monoterpenoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey OZBFUQLOVFXDNK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C12H18O2/c1-7-5-11(14-8(2)13)10-6-9(7)12(10,3)4/h5,9-11H,6H2,1-4H3
SMILES CC1=CC(C2CC1C2(C)C)OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   194.13 Volume:   211.303
?
Van der Waals volume.
Dense:   0.919 LogP:   2.982
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.8
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.55
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   9.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.473 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.613 Fsp3:   0.75
MCE-18:   34.667
?
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:   0.103 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.007
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.706 Promiscuous compounds:   0.403

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.778 MDCK Permeability:   -4.638
Pgp-inhibitor:   0.935 Pgp-substrate:   0.167
PAMPA:   0.236
?
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):   0.241
20% Bioavailability (F20%):   0.519 30% Bioavailability (F30%):   0.602
50% Bioavailability (F50%):   0.863

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.188 MRP1:   0.73
Plasma Protein Binding (PPB):   57.474% Volume Distribution (VD):   0.04
Fu: 41.893%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.939
OATP1B3 inhibitor:   0.933 BCRP inhibitor:   0.075
BSEP inhibitor:   0.816

ADMET: Metabolism

CYP1A2-inhibitor:   0.044 CYP1A2-substrate:   0.654
CYP2C19-inhibitor:   0.903 CYP2C19-substrate:   0.136
CYP2C9-inhibitor:   0.042 CYP2C9-substrate:   0.244
CYP2D6-inhibitor:   0.34 CYP2D6-substrate:   0.287
CYP3A4-inhibitor:   0.508 CYP3A4-substrate:   0.154
CYP2B6-substrate:   0.523 CYP2C8-inhibitor:   0.651
HLM stability:   0.9
?
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):  9.607 Half-life (T1/2):  0.709

ADMET: Toxicity

hERG Blockers:  0.026 hERG Blockers (10um):  0.535
Human Hepatotoxicity (H-HT):  0.436 Drug-induced Liver Injury (DILI):  0.343
AMES Toxicity:  0.165 Rat Oral Acute Toxicity:  0.252
Maximum Recommended Daily Dose:  0.517 Skin Sensitization:  0.67
Carcinogencity:  0.518 Eye Corrosion:  0.631
Eye Irritation:  0.963 Respiratory Toxicity:  0.461
Drug-induced Neurotoxicity:  0.629 Ototoxicity:  0.609
Hematotoxicity:  0.255 Drug-induced Nephrotoxicity:  0.065
Genotoxicity:  0.05 RPMI-8226 Immunitoxicity:  0.027
A549 Cytotoxicity:  0.165 Hek293 Cytotoxicity:  0.113
BCF:   1.655
?
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:   3.95
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.648
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.022
?
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
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2009.03.042]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.3136/fstr.15.499]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB10.140]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB2010.000-3252]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/JMPR.9000078]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. flower n.a. PMID[12130858]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers Tongxiang, China n.a. PMID[24621197]
NPO20874 Tanacetum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25924515]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26099993]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28156114]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28248102]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29400471]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[30726671]
NPO48578 Ducrosia flabellifolia Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36676989]
NPO20874 Tanacetum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37630407]
NPO42417 Achillea vermicularis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38783072]
NPO13182 Achillea wilhelmsii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38783072]
NPO64307 Achillea tenuifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38783072]
NPO13182 Achillea wilhelmsii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39349567]
NPO59027 Pulicaria burchardii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39795328]
NPO13182 Achillea wilhelmsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20874 Tanacetum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20874 Tanacetum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20874 Tanacetum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13182 Achillea wilhelmsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20874 Tanacetum vulgare 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
NPO13182 Achillea wilhelmsii Oil n.a. 0.47 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 0 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 1.37 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 0.99 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 0.12 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 1.36 n.a. n.a. % PMID[38783072]
NPO13182 Achillea wilhelmsii Oil n.a. 0.87 n.a. n.a. % PMID[38783072]
NPO20874 Tanacetum vulgare Oil n.a. 0.47 n.a. n.a. % PMID[37630407]
NPO42417 Achillea vermicularis Oil n.a. 0.33 n.a. n.a. % PMID[38783072]
NPO42417 Achillea vermicularis Oil n.a. 1.28 n.a. n.a. % PMID[38783072]
NPO42417 Achillea vermicularis Oil n.a. 0 n.a. n.a. % PMID[38783072]
NPO48578 Ducrosia flabellifolia Oil n.a. 2.84 n.a. n.a. % PMID[36676989]
NPO59027 Pulicaria burchardii Oil n.a. 0.42 n.a. n.a. % PMID[39795328]
NPO64307 Achillea tenuifolia Oil n.a. 2.04 n.a. n.a. % PMID[38783072]
NPO64307 Achillea tenuifolia Oil n.a. 0 n.a. n.a. % PMID[38783072]
NPO64307 Achillea tenuifolia Oil n.a. 1.24 n.a. n.a. % PMID[38783072]
NPO64307 Achillea tenuifolia Oil n.a. 0.84 n.a. n.a. % PMID[38783072]

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
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 NPC134291 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC134291 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  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