Natural Product: NPC158040

Natural Product IDNPC158040
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QGXIIQMVACEMFG-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5317360
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0001612] Isoflavans
          • [CHEMONTID:0001827] Isoflavanones
            • [CHEMONTID:0003526] 6-prenylated isoflavanones

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 QGXIIQMVACEMFG-UHFFFAOYSA-N
Standard InCHI InChI=1S/C26H26O6/c1-14(2)6-8-17-24-16(10-11-26(3,4)32-24)22(28)21-23(29)18(13-31-25(17)21)15-7-9-19(27)20(12-15)30-5/h6-7,9-13,27-28H,8H2,1-5H3
SMILES CC(=CCc1c2c(C=CC(C)(C)O2)c(c2c(=O)c(coc12)c1ccc(c(c1)OC)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   434.17 Volume:   450.403
?
Van der Waals volume.
Dense:   0.964 LogP:   4.697
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.685
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.238
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   89.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.522 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.185 Fsp3:   0.269
MCE-18:   55.636
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.956 Fluc inhibitor:   0.298
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.831
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.747
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.204 Promiscuous compounds:   0.173

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.977 MDCK Permeability:   -4.654
Pgp-inhibitor:   0.751 Pgp-substrate:   0.011
PAMPA:   0.807
?
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):   0.028
20% Bioavailability (F20%):   0.92 30% Bioavailability (F30%):   0.993
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.011 MRP1:   0.98
Plasma Protein Binding (PPB):   95.163% Volume Distribution (VD):   0.132
Fu: 4.317%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.958
BSEP inhibitor:   0.989

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.993 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.534 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.222 CYP2D6-substrate:   0.148
CYP3A4-inhibitor:   0.506 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
?
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):  3.825 Half-life (T1/2):  1.441

ADMET: Toxicity

hERG Blockers:  0.093 hERG Blockers (10um):  0.58
Human Hepatotoxicity (H-HT):  0.598 Drug-induced Liver Injury (DILI):  0.688
AMES Toxicity:  0.689 Rat Oral Acute Toxicity:  0.808
Maximum Recommended Daily Dose:  0.731 Skin Sensitization:  0.82
Carcinogencity:  0.747 Eye Corrosion:  0.0
Eye Irritation:  0.416 Respiratory Toxicity:  0.921
Drug-induced Neurotoxicity:  0.41 Ototoxicity:  0.481
Hematotoxicity:  0.26 Drug-induced Nephrotoxicity:  0.511
Genotoxicity:  0.734 RPMI-8226 Immunitoxicity:  0.106
A549 Cytotoxicity:  0.27 Hek293 Cytotoxicity:  0.539
BCF:   1.973
?
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:   4.965
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.676
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.025
?
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
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. kernel n.a. PMID[10670815]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. kernel n.a. PMID[12232058]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits Malatya Fruit Research Institute between the first and third weeks of 2005-Jul. PMID[18038980]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. fruit n.a. PMID[21648406]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota Roots n.a. n.a. PMID[24054487]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24412339]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36235013]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. PMID[36675004]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. PMID[37759401]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[38279238]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39181940]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39409699]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39716808]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29051 Ranunculus acris Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11322 Acacia dealbata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7546 Prunus domestica Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7546 Prunus domestica Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7546 Prunus domestica Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7546 Prunus domestica Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11322 Acacia dealbata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29051 Ranunculus acris Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2379 Senecio oryzetorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7546 Prunus domestica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18591 Senecio vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19694 Senecio scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11322 Acacia dealbata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29051 Ranunculus acris Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17962 Tagetes erecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2379 Senecio oryzetorum 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 NPC158040 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
0.8143 Intermediate Similarity NPC237635
0.7917 Intermediate Similarity NPC170026
0.7143 Intermediate Similarity NPC200625
0.6883 Remote Similarity NPC484044
0.6623 Remote Similarity NPC256406
0.6447 Remote Similarity NPC6511
0.642 Remote Similarity NPC188403
0.6329 Remote Similarity NPC201731
0.6282 Remote Similarity NPC610891
0.6173 Remote Similarity NPC282307
0.6145 Remote Similarity NPC28241
0.5976 Remote Similarity NPC79469
0.5765 Remote Similarity NPC470681
0.5663 Remote Similarity NPC327269
0.5663 Remote Similarity NPC244407
0.5663 Remote Similarity NPC204879
0.5581 Remote Similarity NPC91701
0.5422 Remote Similarity NPC214236
0.5357 Remote Similarity NPC184755
0.5357 Remote Similarity NPC31627
0.5357 Remote Similarity NPC14001
0.525 Remote Similarity NPC97716
0.5238 Remote Similarity NPC220418
0.5238 Remote Similarity NPC103238
0.5176 Remote Similarity NPC604254
0.5128 Remote Similarity NPC114192
0.5119 Remote Similarity NPC29876
0.5116 Remote Similarity NPC328102
0.5063 Remote Similarity NPC478987

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC158040 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