Natural Product: NPC218484

Natural Product IDNPC218484
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UPGLJTCDRBIZKP-KYOSRNDESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101596917
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane 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 UPGLJTCDRBIZKP-KYOSRNDESA-N
Standard InCHI InChI=1S/C15H24/c1-10-6-5-8-15(4)9-7-11-13(12(10)15)14(11,2)3/h11,13H,5-9H2,1-4H3/t11-,13-,15+/m1/s1
SMILES CC1=C2[C@H]3[C@@H](CC[C@]2(C)CCC1)C3(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   204.19 Volume:   239.69
?
Van der Waals volume.
Dense:   0.852 LogP:   5.115
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.851
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.45
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   13.0
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:   0.507 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.02 Fsp3:   0.867
MCE-18:   50.214
?
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:   0.271 Fluc inhibitor:   0.026
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.015
?
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:   0.741 Promiscuous compounds:   0.226

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.58 MDCK Permeability:   -4.706
Pgp-inhibitor:   0.706 Pgp-substrate:   0.101
PAMPA:   0.029
?
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%):   0.131 30% Bioavailability (F30%):   0.054
50% Bioavailability (F50%):   0.448

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.96 MRP1:   0.797
Plasma Protein Binding (PPB):   95.32% Volume Distribution (VD):   0.468
Fu: 7.213%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.964
OATP1B3 inhibitor:   0.768 BCRP inhibitor:   0.548
BSEP inhibitor:   0.978

ADMET: Metabolism

CYP1A2-inhibitor:   0.049 CYP1A2-substrate:   0.955
CYP2C19-inhibitor:   0.857 CYP2C19-substrate:   0.189
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.463
CYP2D6-inhibitor:   0.234 CYP2D6-substrate:   0.494
CYP3A4-inhibitor:   0.833 CYP3A4-substrate:   0.965
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.848
HLM stability:   0.835
?
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):  11.276 Half-life (T1/2):  0.741

ADMET: Toxicity

hERG Blockers:  0.124 hERG Blockers (10um):  0.486
Human Hepatotoxicity (H-HT):  0.557 Drug-induced Liver Injury (DILI):  0.21
AMES Toxicity:  0.428 Rat Oral Acute Toxicity:  0.437
Maximum Recommended Daily Dose:  0.569 Skin Sensitization:  0.715
Carcinogencity:  0.714 Eye Corrosion:  0.487
Eye Irritation:  0.935 Respiratory Toxicity:  0.681
Drug-induced Neurotoxicity:  0.433 Ototoxicity:  0.263
Hematotoxicity:  0.293 Drug-induced Nephrotoxicity:  0.315
Genotoxicity:  0.065 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.183 Hek293 Cytotoxicity:  0.314
BCF:   3.358
?
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:   4.667
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.217
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.642
?
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
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. root n.a. DOI[10.1016/S0040-4039(97)10844-9]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. DOI[10.5012/bkcs.2003.24.11.1699]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[12510838]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15165159]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[15646793]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[18404355]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota flowers n.a. n.a. PMID[19374389]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[21657081]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. leaf n.a. PMID[22978234]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. stem n.a. PMID[22978234]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27444348]
NPO28171 Anacyclus pyrethrum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29775308]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota Roots n.a. n.a. PMID[31464439]
NPO60191 Arnica Montana Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31744121]
NPO60191 Arnica Montana Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[32178275]
NPO54179 Magnolia sumatrana var. glauca Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[34328033]
NPO50294 Croton macrostachyus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[35876999]
NPO24292 Plagiochila porelloides Species Plagiochilaceae Eukaryota n.a. n.a. n.a. PMID[36677674]
NPO50294 Croton macrostachyus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[37151484]
NPO28171 Anacyclus pyrethrum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37513251]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37959750]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38538682]
NPO16793 Pittosporum tobira Species Pittosporaceae Eukaryota n.a. n.a. n.a. PMID[38935806]
NPO28171 Anacyclus pyrethrum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39220961]
NPO50294 Croton macrostachyus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28171 Anacyclus pyrethrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16793 Pittosporum tobira Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24292 Plagiochila porelloides Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22666 Haematococcus lacustris Species Haematococcaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28171 Anacyclus pyrethrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16793 Pittosporum tobira Species Pittosporaceae 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
NPO14484 Echinacea purpurea Oil Flowers 0.07 n.a. n.a. % PMID[37959750]
NPO16793 Pittosporum tobira Oil Roots 8.3 n.a. n.a. % PMID[38935806]
NPO24292 Plagiochila porelloides n.a. n.a. 0.1 n.a. n.a. % PMID[36677674]
NPO24292 Plagiochila porelloides n.a. n.a. 0.3 n.a. n.a. % PMID[36677674]
NPO28171 Anacyclus pyrethrum n.a. n.a. 0.4 n.a. n.a. % PMID[39220961]
NPO50294 Croton macrostachyus Oil Seeds 1.5 n.a. n.a. % PMID[37151484]
NPO54179 Magnolia sumatrana var. glauca Oil Bark 0.19 n.a. n.a. % PMID[34328033]
NPO54179 Magnolia sumatrana var. glauca Oil Branches 0.22 n.a. n.a. % PMID[34328033]
NPO60191 Arnica Montana Oil n.a. 0.88 ± 0.11 n.a. n.a. % PMID[31744121]
NPO60191 Arnica Montana Oil n.a. 0.39 ± 0.04 n.a. n.a. % PMID[31744121]

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 NPC218484 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 NPC218484 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