Natural Product: NPC268987

Natural Product IDNPC268987
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SLTLKLCDQWGISZ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 521302
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 SLTLKLCDQWGISZ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H24/c1-10-7-8-15-11(2)5-6-12(9-13(10)15)14(15,3)4/h10,12-13H,2,5-9H2,1,3-4H3
SMILES CC1CCC23C(=C)CCC(CC12)C3(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   204.19 Volume:   239.69
?
Van der Waals volume.
Dense:   0.852 LogP:   4.836
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.757
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.445
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   14.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.513 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.403 Fsp3:   0.867
MCE-18:   70.571
?
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:   0.144 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.771 Promiscuous compounds:   0.01

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.511 MDCK Permeability:   -4.776
Pgp-inhibitor:   0.896 Pgp-substrate:   0.001
PAMPA:   0.002
?
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):   0.002
20% Bioavailability (F20%):   0.005 30% Bioavailability (F30%):   0.026
50% Bioavailability (F50%):   0.574

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.935 MRP1:   0.956
Plasma Protein Binding (PPB):   98.037% Volume Distribution (VD):   0.522
Fu: 2.721%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.715
OATP1B3 inhibitor:   0.954 BCRP inhibitor:   0.185
BSEP inhibitor:   0.961

ADMET: Metabolism

CYP1A2-inhibitor:   0.522 CYP1A2-substrate:   0.573
CYP2C19-inhibitor:   0.989 CYP2C19-substrate:   0.706
CYP2C9-inhibitor:   0.948 CYP2C9-substrate:   0.218
CYP2D6-inhibitor:   0.988 CYP2D6-substrate:   0.04
CYP3A4-inhibitor:   0.567 CYP3A4-substrate:   0.516
CYP2B6-substrate:   0.999 CYP2C8-inhibitor:   0.567
HLM stability:   0.99
?
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):  11.437 Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.156 hERG Blockers (10um):  0.631
Human Hepatotoxicity (H-HT):  0.618 Drug-induced Liver Injury (DILI):  0.239
AMES Toxicity:  0.312 Rat Oral Acute Toxicity:  0.298
Maximum Recommended Daily Dose:  0.685 Skin Sensitization:  0.176
Carcinogencity:  0.58 Eye Corrosion:  0.298
Eye Irritation:  0.912 Respiratory Toxicity:  0.787
Drug-induced Neurotoxicity:  0.673 Ototoxicity:  0.555
Hematotoxicity:  0.281 Drug-induced Nephrotoxicity:  0.126
Genotoxicity:  0.013 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.226 Hek293 Cytotoxicity:  0.315
BCF:   3.094
?
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:   4.865
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.212
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.775
?
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
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50031a011]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[17238120]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18303850]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18405608]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18661821]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18681481]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[19245261]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19344127]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20151678]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21417376]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21627108]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. aerial part n.a. PMID[21902175]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[22472691]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[26000707]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[32119174]
NPO48247 Helichrysum araxinum Takht. ex Kirp. Genus Asteraceae Eukaryota n.a. n.a. n.a. PMID[32619198]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[32880179]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[35481430]
NPO44083 Plectranthus neochilus Genus Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36270431]
NPO54213 Bupleurum lancifolium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36613240]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37446590]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37447270]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37884443]
NPO43140 Eucalyptus woolsiana Genus Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37894690]
NPO59904 Nepeta ucranica Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38035604]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38472808]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38498561]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38681233]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38927152]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39064881]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39065529]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39455637]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[7700984]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[8254353]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20995 Syringa pinnafolia Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44083 Plectranthus neochilus Genus Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33477 Crithmum maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20995 Syringa pinnafolia Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20995 Syringa pinnafolia Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29016 Valeriana jatamansi Species Caprifoliaceae 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
NPO33477 Crithmum maritimum Oil n.a. 0.9 n.a. n.a. % PMID[32119174]
NPO43140 Eucalyptus woolsiana Oil n.a. 1.3 n.a. n.a. % PMID[37894690]
NPO44083 Plectranthus neochilus Oil n.a. 2.94 n.a. n.a. % PMID[36270431]
NPO44083 Plectranthus neochilus Oil n.a. 3.2 n.a. n.a. % PMID[36270431]
NPO48247 Helichrysum araxinum Takht. ex Kirp. Oil n.a. 2.0±0.06 n.a. n.a. % PMID[32619198]
NPO54213 Bupleurum lancifolium n.a. Aerial parts 23.79 n.a. n.a. % PMID[36613240]
NPO59904 Nepeta ucranica Oil n.a. 8.8 n.a. n.a. % PMID[38035604]
NPO7513 Cannabis sativa Oil n.a. 0.47 ± 0.01 n.a. n.a. % PMID[38927152]

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 NPC268987 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 NPC268987 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