Natural Product: NPC113662

Natural Product IDNPC113662
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 TYUXEIYWRBFXFZ-RTRCTDTCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12000325
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

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 TYUXEIYWRBFXFZ-RTRCTDTCSA-N
Standard InCHI InChI=1S/C20H24O6/c1-9(2)13-7-6-12-8-14(26-20(12)25)15(10(3)4)19(24)17(22)11(5)16(21)18(13)23/h8,13-15,18,22-23H,1,3,6-7H2,2,4-5H3/b17-11+/t13-,14+,15+,18-/m0/s1
SMILES C=C(C)[C@@H]1CCC2=C[C@H]([C@@H](C(=C)C)C(=O)/C(=C(/C)C(=O)[C@H]1O)/O)OC2=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   360.16 Volume:   371.649
?
Van der Waals volume.
Dense:   0.969 LogP:   1.193
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.518
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.844
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   20.0
TPSA:   100.9
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.579 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.892 Fsp3:   0.45
MCE-18:   43.448
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.599 Fluc inhibitor:   0.422
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.108
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.057
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.508 Promiscuous compounds:   0.273

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.843 MDCK Permeability:   -4.547
Pgp-inhibitor:   0.866 Pgp-substrate:   0.001
PAMPA:   0.124
?
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%):   0.004 30% Bioavailability (F30%):   0.327
50% Bioavailability (F50%):   0.887

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.046 MRP1:   0.952
Plasma Protein Binding (PPB):   87.169% Volume Distribution (VD):   -0.053
Fu: 8.687%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.583
BSEP inhibitor:   0.982

ADMET: Metabolism

CYP1A2-inhibitor:   0.003 CYP1A2-substrate:   0.206
CYP2C19-inhibitor:   0.01 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.008 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.067
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.016
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.862
HLM stability:   0.8
?
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):  5.189 Half-life (T1/2):  1.648

ADMET: Toxicity

hERG Blockers:  0.008 hERG Blockers (10um):  0.037
Human Hepatotoxicity (H-HT):  0.673 Drug-induced Liver Injury (DILI):  0.923
AMES Toxicity:  0.349 Rat Oral Acute Toxicity:  0.251
Maximum Recommended Daily Dose:  0.113 Skin Sensitization:  0.977
Carcinogencity:  0.496 Eye Corrosion:  0.083
Eye Irritation:  0.97 Respiratory Toxicity:  0.159
Drug-induced Neurotoxicity:  0.086 Ototoxicity:  0.767
Hematotoxicity:  0.782 Drug-induced Nephrotoxicity:  0.765
Genotoxicity:  0.91 RPMI-8226 Immunitoxicity:  0.043
A549 Cytotoxicity:  0.018 Hek293 Cytotoxicity:  0.029
BCF:   1.316
?
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:   3.955
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.791
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.039
?
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
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[10395513]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[15182859]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. root n.a. PMID[16310231]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. root n.a. PMID[16651783]
NPO24654 Curculigo crassifolia Species Hypoxidaceae Eukaryota n.a. rhizome n.a. PMID[18958422]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[21090694]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. stem n.a. PMID[21428375]
NPO25544 Encyclia michuacana Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[21510636]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[23599008]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[24175613]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26351040]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[34203980]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[37894884]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. PMID[9644074]
NPO26421 Urtica laetevirens Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17597 Cassia fistulosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24787 Astragalus babatagi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18878.1 Amaranthus blitum subsp. oleraceus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25442 Isocoma tenuisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24562 Saussurea petrovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3843 Rhododendron metternichii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25544 Encyclia michuacana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25930 Cystoseira balearica Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24654 Curculigo crassifolia Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25527 Tephrosia multijuga Species Geometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24210 Senecio heterotrichus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18873.7 Salmonella enterica subsp. enterica serovar typhi Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO20129 Salicornia europaea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21817 Riccardia chamedryfolia Species Aneuraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24474 Rhododendron lepidotum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21476 Pterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24741 Psathyrella scobinacea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15326 Paranemertes peregrina Species n.a. Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19851 Miconia stenostachya Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24985 Lippia asperifolia Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24562 Saussurea petrovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18878.1 Amaranthus blitum subsp. oleraceus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26421 Urtica laetevirens Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24985 Lippia asperifolia Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24654 Curculigo crassifolia Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17597 Cassia fistulosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3843 Rhododendron metternichii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25930 Cystoseira balearica Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19851 Miconia stenostachya Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24474 Rhododendron lepidotum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24741 Psathyrella scobinacea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18878.1 Amaranthus blitum subsp. oleraceus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21476 Pterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24562 Saussurea petrovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25442 Isocoma tenuisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20129 Salicornia europaea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.7 Salmonella enterica subsp. enterica serovar typhi Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24787 Astragalus babatagi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21817 Riccardia chamedryfolia Species Aneuraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25527 Tephrosia multijuga Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25544 Encyclia michuacana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15326 Paranemertes peregrina Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24210 Senecio heterotrichus 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 NPC113662 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
0.6034 Remote Similarity NPC605132

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC113662 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