Natural Product: NPC242991

Natural Product IDNPC242991
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YNJGXQUTVLYUEZ-QUJJFIQJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 25259221
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001816] Furofurans

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 YNJGXQUTVLYUEZ-QUJJFIQJSA-N
Standard InCHI InChI=1S/C26H38O5/c1-18(2)9-8-12-24(5)13-10-20-17-30-22-16-25(6,28-7)31-26(20,22)21(24)11-14-29-23(27)15-19(3)4/h9-11,14-15,21-22H,8,12-13,16-17H2,1-7H3/b14-11+/t21-,22+,24+,25+,26-/m1/s1
SMILES CC(=CCC[C@@]1(C)CC=C2CO[C@H]3C[C@@](C)(OC)O[C@@]23[C@@H]1/C=C/OC(=O)C=C(C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   430.27 Volume:   463.352
?
Van der Waals volume.
Dense:   0.929 LogP:   4.618
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.804
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.028
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   18.0
TPSA:   53.99
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.227 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.784 Fsp3:   0.654
MCE-18:   80.93
?
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:   0.375 Fluc inhibitor:   0.018
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.015
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.432 Promiscuous compounds:   0.081

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.782 MDCK Permeability:   -4.722
Pgp-inhibitor:   0.417 Pgp-substrate:   0.139
PAMPA:   0.369
?
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%):   0.021 30% Bioavailability (F30%):   0.014
50% Bioavailability (F50%):   0.611

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.508 MRP1:   0.943
Plasma Protein Binding (PPB):   96.9% Volume Distribution (VD):   0.33
Fu: 3.129%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.983
OATP1B3 inhibitor:   0.937 BCRP inhibitor:   0.021
BSEP inhibitor:   0.956

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.991
CYP2C19-inhibitor:   0.955 CYP2C19-substrate:   0.052
CYP2C9-inhibitor:   0.004 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.014 CYP2D6-substrate:   0.019
CYP3A4-inhibitor:   0.36 CYP3A4-substrate:   0.658
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.516
HLM stability:   0.988
?
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):  9.134 Half-life (T1/2):  0.833

ADMET: Toxicity

hERG Blockers:  0.193 hERG Blockers (10um):  0.609
Human Hepatotoxicity (H-HT):  0.459 Drug-induced Liver Injury (DILI):  0.504
AMES Toxicity:  0.663 Rat Oral Acute Toxicity:  0.784
Maximum Recommended Daily Dose:  0.74 Skin Sensitization:  0.965
Carcinogencity:  0.334 Eye Corrosion:  0.007
Eye Irritation:  0.367 Respiratory Toxicity:  0.827
Drug-induced Neurotoxicity:  0.866 Ototoxicity:  0.541
Hematotoxicity:  0.463 Drug-induced Nephrotoxicity:  0.448
Genotoxicity:  0.293 RPMI-8226 Immunitoxicity:  0.169
A549 Cytotoxicity:  0.165 Hek293 Cytotoxicity:  0.316
BCF:   2.256
?
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:   4.963
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.539
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.113
?
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
NPO6082 Centaurium pulchellum Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)83457-3]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10075772]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[10843567]
NPO6717 Viburnum awabuki Species Adoxaceae Eukaryota n.a. n.a. n.a. PMID[15043405]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[16155971]
NPO4979 Elysia grandifolia Species Placobranchidae Eukaryota n.a. n.a. n.a. PMID[17125219]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17665952]
NPO8269 Isodon nervosus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18345641]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19824618]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[21667999]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. latex n.a. PMID[21854017]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[22703163]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[24328283]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[24704554]
NPO7935 Strychnos angustiflora Species Loganiaceae Eukaryota n.a. n.a. n.a. PMID[27592135]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[324959]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32935986]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[33325237]
NPO6717 Viburnum awabuki Species Adoxaceae Eukaryota n.a. leaf n.a. Database[Article]
NPO5144 Berberis japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10806 Achillea roseoalba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1355 Urechis caupo Species Urechidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5319 Ulmus thomasii Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7935 Strychnos angustiflora Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6310 Ruta bracteosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7766 Pericopsis schliebenii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9228.1 Narcissus pseudonarcissus subsp. leonensis Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO276 Miscanthus sacchariflorus Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25481 Lonchocarpus oaxacensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8103 Lecanora melanophthalma Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8269 Isodon nervosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2637 Agave rigidissima Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7060 Ficus ruficaulis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4516 Fasciospongia rimosa Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3830 Euplotes rariseta Species Euplotidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9903 Engelhardia spicata Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4979 Elysia grandifolia Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24370 Crassocephalum crepidioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15610 Citrus trifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6082 Centaurium pulchellum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2304 Byssovorax cruenta Species Polyangiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6717 Viburnum awabuki Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7935 Strychnos angustiflora Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5144 Berberis japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2637 Agave rigidissima Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7935 Strychnos angustiflora Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9228.1 Narcissus pseudonarcissus subsp. leonensis Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6717 Viburnum awabuki Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8911 Aspergillus aculeatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6717 Viburnum awabuki Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7060 Ficus ruficaulis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4516 Fasciospongia rimosa Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO276 Miscanthus sacchariflorus Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5144 Berberis japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9228.1 Narcissus pseudonarcissus subsp. leonensis Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8404 Isodon xerophilus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10806 Achillea roseoalba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1355 Urechis caupo Species Urechidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5319 Ulmus thomasii Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25481 Lonchocarpus oaxacensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7935 Strychnos angustiflora Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7766 Pericopsis schliebenii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8103 Lecanora melanophthalma Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9903 Engelhardia spicata Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2304 Byssovorax cruenta Species Polyangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2637 Agave rigidissima Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4979 Elysia grandifolia Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15610 Citrus trifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24370 Crassocephalum crepidioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6082 Centaurium pulchellum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3830 Euplotes rariseta Species Euplotidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6310 Ruta bracteosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8269 Isodon nervosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8911 Aspergillus aculeatus Species Aspergillaceae 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 NPC242991 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 NPC242991 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