Natural Product: NPC151879

Natural Product IDNPC151879
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ULJUKDKFFCRJPF-GNADVCDUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 71620321
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

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 ULJUKDKFFCRJPF-GNADVCDUSA-N
Standard InCHI InChI=1S/C24H28O9/c1-30-14-5-6-15-12(7-14)3-4-13(16-9-19(31-2)18(26)8-17(15)16)11-32-24-23(29)22(28)21(27)20(10-25)33-24/h4-9,20-29H,3,10-11H2,1-2H3/t20-,21-,22+,23-,24-/m1/s1
SMILES COc1ccc2-c3cc(c(cc3C(=CCc2c1)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   460.17 Volume:   450.091
?
Van der Waals volume.
Dense:   1.022 LogP:   1.925
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.247
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.531
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   23.0
TPSA:   138.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   5.0 Rings:   4.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.424 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.034 Fsp3:   0.417
MCE-18:   83.824
?
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:   0.658 Fluc inhibitor:   0.189
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.748
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.407
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.069 Promiscuous compounds:   0.124

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.974 MDCK Permeability:   -5.08
Pgp-inhibitor:   0.004 Pgp-substrate:   0.473
PAMPA:   0.589
?
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):   0.857
20% Bioavailability (F20%):   0.266 30% Bioavailability (F30%):   0.962
50% Bioavailability (F50%):   0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.336
Plasma Protein Binding (PPB):   89.605% Volume Distribution (VD):   -0.286
Fu: 11.43%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.571
BSEP inhibitor:   0.019

ADMET: Metabolism

CYP1A2-inhibitor:   0.989 CYP1A2-substrate:   0.001
CYP2C19-inhibitor:   0.999 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.999 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.64 CYP2D6-substrate:   0.757
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.25
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.707
?
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):  3.113 Half-life (T1/2):  2.635

ADMET: Toxicity

hERG Blockers:  0.197 hERG Blockers (10um):  0.192
Human Hepatotoxicity (H-HT):  0.759 Drug-induced Liver Injury (DILI):  0.865
AMES Toxicity:  0.959 Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.29 Skin Sensitization:  0.935
Carcinogencity:  0.53 Eye Corrosion:  0.0
Eye Irritation:  0.011 Respiratory Toxicity:  0.183
Drug-induced Neurotoxicity:  0.26 Ototoxicity:  0.974
Hematotoxicity:  0.478 Drug-induced Nephrotoxicity:  0.883
Genotoxicity:  0.734 RPMI-8226 Immunitoxicity:  0.303
A549 Cytotoxicity:  0.87 Hek293 Cytotoxicity:  0.729
BCF:   0.877
?
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:   3.466
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.036
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.195
?
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
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. PMID[10924179]
NPO8035 Tylophora tanakae Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12350151]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stems Wulai Hsiang, Taipei County, Taiwan 2005-MAY PMID[17253858]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19581087]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[20299229]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota bark n.a. n.a. PMID[20363129]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21214253]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota Leaves n.a. n.a. PMID[23025417]
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. PMID[23131412]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stem bark Laifeng, Hubei Province, China 2012-JUL PMID[26087384]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota Fruit juice n.a. n.a. PMID[3404148]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3378 Alstonia undulifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10737 Asteriscus aquaticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11811 Capparis ovata Species Capparaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12669 Cassine papillosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9509 Charpentiera obovata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15252 Clathria prolifera Species Microcionidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6253 Conus pulicarius Species Conidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1182 Croton montevidensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12188 Datisca glomerata Species Datiscaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12888 Echinus microtuberculatus Species Echinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10393 Ophidiaster ophidianus Species Ophidiasteridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7045 Viviparus japonicus Species Viviparidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8035 Tylophora tanakae Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7709 Spiracantha cornifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2608 Solanum andigena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3736 Scrophularia koelzii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12436 Quercus imbricaria Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11256 Pseudowintera colorata Species Winteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4493 Polygonum flaccidum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20291 Phyllanthus oligospermus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11553 Phebalium dentatum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12544 Dioscorea olfersiana Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8477 Myristica cagayanensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9922 Myelobia smerintha Species Crambidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12308 Metridium senile Species Metridiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9672 Lotus ucrainicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5384 Ligustrum obtusifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5008 Hubertia tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5823 Helichrysum auriceps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO761 Fagus fusca Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12308 Metridium senile Species Metridiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8477 Myristica cagayanensis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1182 Croton montevidensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11811 Capparis ovata Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4493 Polygonum flaccidum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10393 Ophidiaster ophidianus Species Ophidiasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2608 Solanum andigena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9672 Lotus ucrainicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7709 Spiracantha cornifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9922 Myelobia smerintha Species Crambidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5823 Helichrysum auriceps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9305 Iotrochota purpurea Species Iotrochotidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12544 Dioscorea olfersiana Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4138 Betula platyphylla Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11699 Ecballium elaterium Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12436 Quercus imbricaria Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO761 Fagus fusca Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8035 Tylophora tanakae Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5008 Hubertia tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20291 Phyllanthus oligospermus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2298 Streptomyces platensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12669 Cassine papillosa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12888 Echinus microtuberculatus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3378 Alstonia undulifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15252 Clathria prolifera Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9509 Charpentiera obovata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6253 Conus pulicarius Species Conidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7045 Viviparus japonicus Species Viviparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12188 Datisca glomerata Species Datiscaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3736 Scrophularia koelzii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11553 Phebalium dentatum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10737 Asteriscus aquaticus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11256 Pseudowintera colorata Species Winteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5384 Ligustrum obtusifolium Species Oleaceae 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 NPC151879 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
0.8082 Intermediate Similarity NPC48309
0.6765 Remote Similarity NPC106511
0.6375 Remote Similarity NPC76871

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC151879 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