Natural Product: NPC34247

Natural Product IDNPC34247
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HMLGXKHWABZSIS-YWPYICTPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5317414
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane 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 HMLGXKHWABZSIS-YWPYICTPSA-N
Standard InCHI InChI=1S/C15H24O/c1-10(2)13-9-15(4)11(3)6-5-7-12(15)8-14(13)16/h11-12H,5-9H2,1-4H3/t11-,12+,15+/m0/s1
SMILES CC(=C1C[C@]2(C)[C@@H](C)CCC[C@@H]2CC1=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   220.18 Volume:   254.401
?
Van der Waals volume.
Dense:   0.865 LogP:   3.83
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.515
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.037
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   13.0
TPSA:   17.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.561 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.871 Fsp3:   0.8
MCE-18:   36.296
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.082 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.012
?
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:   0.984 Promiscuous compounds:   0.404

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.692 MDCK Permeability:   -4.923
Pgp-inhibitor:   0.98 Pgp-substrate:   0.029
PAMPA:   0.072
?
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):   0.014
20% Bioavailability (F20%):   0.09 30% Bioavailability (F30%):   0.297
50% Bioavailability (F50%):   0.814

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.67 MRP1:   0.938
Plasma Protein Binding (PPB):   82.019% Volume Distribution (VD):   0.51
Fu: 19.198%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.985
OATP1B3 inhibitor:   0.977 BCRP inhibitor:   0.107
BSEP inhibitor:   0.976

ADMET: Metabolism

CYP1A2-inhibitor:   0.953 CYP1A2-substrate:   0.465
CYP2C19-inhibitor:   0.993 CYP2C19-substrate:   0.042
CYP2C9-inhibitor:   0.03 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.313 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.655 CYP3A4-substrate:   0.971
CYP2B6-substrate:   0.566 CYP2C8-inhibitor:   0.094
HLM stability:   0.979
?
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):  11.062 Half-life (T1/2):  0.885

ADMET: Toxicity

hERG Blockers:  0.074 hERG Blockers (10um):  0.336
Human Hepatotoxicity (H-HT):  0.69 Drug-induced Liver Injury (DILI):  0.52
AMES Toxicity:  0.532 Rat Oral Acute Toxicity:  0.299
Maximum Recommended Daily Dose:  0.487 Skin Sensitization:  0.826
Carcinogencity:  0.875 Eye Corrosion:  0.827
Eye Irritation:  0.954 Respiratory Toxicity:  0.777
Drug-induced Neurotoxicity:  0.43 Ototoxicity:  0.324
Hematotoxicity:  0.514 Drug-induced Nephrotoxicity:  0.58
Genotoxicity:  0.156 RPMI-8226 Immunitoxicity:  0.071
A549 Cytotoxicity:  0.169 Hek293 Cytotoxicity:  0.195
BCF:   1.838
?
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:   4.032
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.158
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.748
?
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
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[12662092]
NPO8076 Viburnum luzonicum Species Adoxaceae Eukaryota n.a. n.a. n.a. PMID[15568771]
NPO8076 Viburnum luzonicum Species Adoxaceae Eukaryota n.a. leaf n.a. PMID[15635247]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. PMID[15679308]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. Caribbean n.a. PMID[1686898]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. stem n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[21226514]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[26281591]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[3404159]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[37988956]
NPO8076 Viburnum luzonicum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1049 Tethya amamensis Species Tethyidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7793 Matricaria matricarioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO117 Acacia armata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO643 Astragalus ernestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8433 Bongardia chrysogonum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2008 Streptomyces ehimensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO8950 Stilpnopappus pickelii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1203 Solanum pseudoquina Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4836 Sideritis arborescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2323 Plantago lundborgii Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19991 Mantella aurantiaca Species Mantellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13682 Lonchocarpus laxiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5339 Isophysis tasmanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8132 Fritillaria meleagris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1706 Eragrostis curvula Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17179 Elizabethkingia meningoseptica Species Flavobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3445 Dumoria heckeli n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1541 Clusia ellipticifolia Species Clusiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO21493 Bunodosoma caissarum Species Actiniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota Pt n.a. n.a. Database[FooDB]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8076 Viburnum luzonicum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8950 Stilpnopappus pickelii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5339 Isophysis tasmanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2323 Plantago lundborgii Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19991 Mantella aurantiaca Species Mantellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7793 Matricaria matricarioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1049 Tethya amamensis Species Tethyidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21493 Bunodosoma caissarum Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8132 Fritillaria meleagris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1706 Eragrostis curvula Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13682 Lonchocarpus laxiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1541 Clusia ellipticifolia Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17179 Elizabethkingia meningoseptica Species Flavobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20047 Aconitum tuberosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1203 Solanum pseudoquina Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8433 Bongardia chrysogonum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO117 Acacia armata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2008 Streptomyces ehimensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4836 Sideritis arborescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO643 Astragalus ernestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6148 Aesculus glabra Species Hippocastanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3445 Dumoria heckeli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2264 Salvia mexicana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7008 Coniogramme intermedia Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8076 Viburnum luzonicum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26311 Panicum virgatum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10980 Petasites japonicus 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

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 NPC34247 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 NPC34247 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