Natural Product: NPC240336

Natural Product IDNPC240336
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UWOCAPHKEVQLDY-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002595] 3'-O-methylated flavonoids

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 UWOCAPHKEVQLDY-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O6/c1-8-3-9(4-15(22-2)17(8)21)13-7-12(20)16-11(19)5-10(18)6-14(16)23-13/h3-7,18-19,21H,1-2H3
SMILES Cc1cc(cc(c1O)OC)c1cc(=O)c2c(cc(cc2o1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   314.08 Volume:   308.569
?
Van der Waals volume.
Dense:   1.018 LogP:   2.936
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.373
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.444
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   100.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.672 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.481 Fsp3:   0.118
MCE-18:   19.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.684 Fluc inhibitor:   0.644
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.961
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.749
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.455 Promiscuous compounds:   0.482

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.063 MDCK Permeability:   -4.828
Pgp-inhibitor:   0.417 Pgp-substrate:   0.26
PAMPA:   0.094
?
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):   0.01
20% Bioavailability (F20%):   0.217 30% Bioavailability (F30%):   0.647
50% Bioavailability (F50%):   0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.011 MRP1:   0.91
Plasma Protein Binding (PPB):   98.284% Volume Distribution (VD):   -0.448
Fu: 1.116%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.992
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.992
BSEP inhibitor:   0.954

ADMET: Metabolism

CYP1A2-inhibitor:   0.986 CYP1A2-substrate:   0.855
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.133
CYP2C9-inhibitor:   0.891 CYP2C9-substrate:   0.962
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.35
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.996
HLM stability:   0.445
?
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):  5.278 Half-life (T1/2):  1.193

ADMET: Toxicity

hERG Blockers:  0.068 hERG Blockers (10um):  0.505
Human Hepatotoxicity (H-HT):  0.423 Drug-induced Liver Injury (DILI):  0.701
AMES Toxicity:  0.619 Rat Oral Acute Toxicity:  0.505
Maximum Recommended Daily Dose:  0.846 Skin Sensitization:  0.647
Carcinogencity:  0.774 Eye Corrosion:  0.514
Eye Irritation:  0.997 Respiratory Toxicity:  0.823
Drug-induced Neurotoxicity:  0.066 Ototoxicity:  0.084
Hematotoxicity:  0.09 Drug-induced Nephrotoxicity:  0.044
Genotoxicity:  0.94 RPMI-8226 Immunitoxicity:  0.081
A549 Cytotoxicity:  0.327 Hek293 Cytotoxicity:  0.717
BCF:   0.961
?
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:   3.737
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.494
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.923
?
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
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1104/pp.84.1.73]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11599360]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[12081149]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12232319]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. aerial part n.a. PMID[1442064]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[15635251]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20000780]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. seed n.a. PMID[21381697]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. root n.a. PMID[22051934]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22208890]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[24660446]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota aerial parts herbal garden of Chungbuk National University, Cheongju, Korea 2012-Oct PMID[24963714]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[36300020]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37120447]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[501363]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[7320737]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. aerial part n.a. Database[Article]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31185 Phragmites communis Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31185 Phragmites communis Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21939 Phyllostachys nigra Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31185 Phragmites communis Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28569 Epimedium acuminatum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19755 Artemisia anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8210 Trigonella foenum-graecum 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

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 NPC240336 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
0.75 Intermediate Similarity NPC120464
0.7 Intermediate Similarity NPC183950
0.6897 Remote Similarity NPC62536
0.6897 Remote Similarity NPC483773
0.661 Remote Similarity NPC231772
0.661 Remote Similarity NPC601901
0.6557 Remote Similarity NPC52005
0.6557 Remote Similarity NPC12200
0.6557 Remote Similarity NPC606638
0.623 Remote Similarity NPC600900
0.5862 Remote Similarity NPC50898
0.5862 Remote Similarity NPC78540
0.5797 Remote Similarity NPC183
0.5763 Remote Similarity NPC175013
0.5758 Remote Similarity NPC605634
0.5667 Remote Similarity NPC279121
0.5645 Remote Similarity NPC605617
0.5556 Remote Similarity NPC28274
0.5541 Remote Similarity NPC63454
0.5541 Remote Similarity NPC183851
0.5455 Remote Similarity NPC133953
0.541 Remote Similarity NPC274121
0.5397 Remote Similarity NPC284552
0.5373 Remote Similarity NPC483775
0.5342 Remote Similarity NPC134796
0.5323 Remote Similarity NPC213216
0.5316 Remote Similarity NPC101731
0.5312 Remote Similarity NPC48479
0.5286 Remote Similarity NPC301217
0.5278 Remote Similarity NPC224714
0.527 Remote Similarity NPC150908
0.527 Remote Similarity NPC600972
0.525 Remote Similarity NPC165970
0.525 Remote Similarity NPC172202
0.525 Remote Similarity NPC284127
0.5238 Remote Similarity NPC610974
0.5224 Remote Similarity NPC125062
0.5224 Remote Similarity NPC279989
0.52 Remote Similarity NPC290830
0.52 Remote Similarity NPC71061
0.52 Remote Similarity NPC72425
0.52 Remote Similarity NPC303485
0.5185 Remote Similarity NPC288131
0.5156 Remote Similarity NPC219330
0.5152 Remote Similarity NPC83508
0.5132 Remote Similarity NPC272064
0.5132 Remote Similarity NPC186227
0.5077 Remote Similarity NPC610359
0.5075 Remote Similarity NPC162351
0.5075 Remote Similarity NPC609179
0.507 Remote Similarity NPC112954
0.5065 Remote Similarity NPC215203
0.506 Remote Similarity NPC84324

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC240336 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
0.5667 Remote Similarity NPD1511 Phase 2

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