Natural Product: NPC259631

Natural Product IDNPC259631
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZAJTXVHECZCXLH-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 177040
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0003522] 2,2-dimethyl-1-benzopyrans

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 ZAJTXVHECZCXLH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C13H14O2/c1-9(14)10-4-5-12-11(8-10)6-7-13(2,3)15-12/h4-8H,1-3H3
SMILES CC(=O)c1ccc2c(C=CC(C)(C)O2)c1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   202.1 Volume:   220.69
?
Van der Waals volume.
Dense:   0.916 LogP:   2.967
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.001
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.275
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   12.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.654 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.444 Fsp3:   0.308
MCE-18:   27.529
?
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:   0.19 Fluc inhibitor:   0.025
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.21
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.144
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.889 Promiscuous compounds:   0.268

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.442 MDCK Permeability:   -4.653
Pgp-inhibitor:   0.744 Pgp-substrate:   0.097
PAMPA:   0.199
?
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):   0.017
20% Bioavailability (F20%):   0.238 30% Bioavailability (F30%):   0.439
50% Bioavailability (F50%):   0.847

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.866 MRP1:   0.761
Plasma Protein Binding (PPB):   93.554% Volume Distribution (VD):   0.24
Fu: 5.694%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.89
OATP1B3 inhibitor:   0.909 BCRP inhibitor:   0.597
BSEP inhibitor:   0.928

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.012 CYP2C19-substrate:   0.835
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.161
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.151
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.225
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.998
HLM stability:   0.916
?
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):  8.27 Half-life (T1/2):  0.772

ADMET: Toxicity

hERG Blockers:  0.16 hERG Blockers (10um):  0.494
Human Hepatotoxicity (H-HT):  0.537 Drug-induced Liver Injury (DILI):  0.329
AMES Toxicity:  0.714 Rat Oral Acute Toxicity:  0.44
Maximum Recommended Daily Dose:  0.31 Skin Sensitization:  0.431
Carcinogencity:  0.795 Eye Corrosion:  0.326
Eye Irritation:  0.964 Respiratory Toxicity:  0.835
Drug-induced Neurotoxicity:  0.635 Ototoxicity:  0.326
Hematotoxicity:  0.451 Drug-induced Nephrotoxicity:  0.319
Genotoxicity:  0.355 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.059 Hek293 Cytotoxicity:  0.206
BCF:   0.915
?
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:   3.522
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.751
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.241
?
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
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. small food enterprises (Zvijezda d.d., Zagreb, Croatia) n.a. DOI[10.1002/EJLT.200900231]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. n.a. PMID[12542343]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota roots n.a. n.a. PMID[14664512]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16660462]
NPO454 Helianthus annuus Species Asteraceae Eukaryota flower petals n.a. n.a. PMID[17480100]
NPO19134 Boronia bipinnata Species Rutaceae Eukaryota n.a. aerial part n.a. PMID[18662038]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. seed n.a. PMID[25172742]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37939623]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38810900]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[6361218]
NPO28004 Pseudodistoma megalarva Species Pseudodistomidae Eukaryota n.a. n.a. n.a. PMID[9358640]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. n.a. PMID[9677276]
NPO16661 Duboisia myoporoides Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11052 Helianthus hirsutus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26523 Alicyclobacillus acidocaldarius Species Alicyclobacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO19134 Boronia bipinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8147 Calea hispida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22725 Cirsium microspicatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17194 Linum capitatum Species Linaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18310 Pecten jacobaeus Species Pectinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13648 Phialocephala fortinii Species n.a. Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28004 Pseudodistoma megalarva Species Pseudodistomidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17285 Taraxacum udum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15676 Tricholoma scalpturatum Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15368 Trifolium medium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9379 Cytisus caucasicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10414 Gram-negative bacterium n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Flower Essent. Oil n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO454 Helianthus annuus Species Asteraceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19134 Boronia bipinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13648 Phialocephala fortinii Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15676 Tricholoma scalpturatum Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18310 Pecten jacobaeus Species Pectinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22725 Cirsium microspicatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO454 Helianthus annuus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26371 Sorghum bicolor Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26523 Alicyclobacillus acidocaldarius Species Alicyclobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17285 Taraxacum udum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8147 Calea hispida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28004 Pseudodistoma megalarva Species Pseudodistomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16661 Duboisia myoporoides Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15368 Trifolium medium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10414 Gram-negative bacterium n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17194 Linum capitatum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11052 Helianthus hirsutus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9379 Cytisus caucasicus Species Fabaceae 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
NPO23234 Ageratum conyzoides Oil n.a. 1.19 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.38 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.33 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.39 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.42 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.55 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.7 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.32 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.52 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.67 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.73 n.a. n.a. % PMID[38810900]
NPO23234 Ageratum conyzoides Oil n.a. 0.54 n.a. n.a. % PMID[38810900]
NPO454 Helianthus annuus Other Root 1 1 1 mg/100g Database [DUKE]

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
NPT28438 Unchecked Unchecked n.a. IC50 = 459630.0 nM PMID[33857371]

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 NPC259631 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
0.6923 Remote Similarity NPC608132
0.6585 Remote Similarity NPC161696
0.6429 Remote Similarity NPC90903
0.6341 Remote Similarity NPC229646
0.6279 Remote Similarity NPC165556
0.6047 Remote Similarity NPC151113
0.5455 Remote Similarity NPC142595
0.5455 Remote Similarity NPC609025
0.5455 Remote Similarity NPC609512
0.5349 Remote Similarity NPC106141
0.5192 Remote Similarity NPC283079
0.5091 Remote Similarity NPC59522
0.5091 Remote Similarity NPC235239

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC259631 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