Natural Product: NPC277570

Natural Product IDNPC277570
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 8E-Decaene-4,6-Diyn-1-O-Beta-D-Glucopyranoside
IUPAC Name (2R,3R,4S,5S,6R)-2-[(E)-dec-8-en-4,6-diynoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2011519
PubChem CID 70695725
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

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 QIFYDSMWESCVBZ-FAOXUISGSA-N
Standard InCHI InChI=1S/C16H22O6/c1-2-3-4-5-6-7-8-9-10-21-16-15(20)14(19)13(18)12(11-17)22-16/h2-3,12-20H,8-11H2,1H3/b3-2+/t12-,13-,14+,15-,16-/m1/s1
SMILES C/C=C/C#CC#CCCCO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   310.14 Volume:   316.295
?
Van der Waals volume.
Dense:   0.981 LogP:   0.758
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.023
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.385
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   9.0
TPSA:   99.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.391 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.431 Fsp3:   0.625
MCE-18:   19.077
?
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:   0.195 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.339 Promiscuous compounds:   0.012

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.33 MDCK Permeability:   -4.888
Pgp-inhibitor:   0.018 Pgp-substrate:   0.001
PAMPA:   1.0
?
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):   0.082
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.006
50% Bioavailability (F50%):   0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   86.502% Volume Distribution (VD):   -0.37
Fu: 8.395%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.265
OATP1B3 inhibitor:   0.574 BCRP inhibitor:   0.982
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.416 CYP1A2-substrate:   0.096
CYP2C19-inhibitor:   0.545 CYP2C19-substrate:   0.675
CYP2C9-inhibitor:   0.007 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.334
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.423
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.311
?
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):  3.171 Half-life (T1/2):  1.897

ADMET: Toxicity

hERG Blockers:  0.032 hERG Blockers (10um):  0.165
Human Hepatotoxicity (H-HT):  0.584 Drug-induced Liver Injury (DILI):  0.834
AMES Toxicity:  0.84 Rat Oral Acute Toxicity:  0.065
Maximum Recommended Daily Dose:  0.061 Skin Sensitization:  0.995
Carcinogencity:  0.33 Eye Corrosion:  0.045
Eye Irritation:  0.709 Respiratory Toxicity:  0.349
Drug-induced Neurotoxicity:  0.03 Ototoxicity:  0.888
Hematotoxicity:  0.192 Drug-induced Nephrotoxicity:  0.459
Genotoxicity:  0.016 RPMI-8226 Immunitoxicity:  0.086
A549 Cytotoxicity:  0.089 Hek293 Cytotoxicity:  0.298
BCF:   0.51
?
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:   3.144
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.732
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.762
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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
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[17262892]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[21163339]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22060189]
NPO23708 Aster koraiensis Species Asteraceae Eukaryota aerial parts Euidang-myun, Gongju city, Chungchengnam-do, Republic of Korea 2007-Aug PMID[22264115]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. flower n.a. PMID[22723874]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23371463]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flowers Lasa, China n.a. PMID[24621197]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27748595]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37446759]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39732883]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Bud n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5406 Veronica chamaedrys Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9385 Glycosmis ovoidea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14084 Roccella fucoides Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2509 Strombus gigas Species Strombidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO368 Dendroaspis angusticeps Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23708 Aster koraiensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18458 Raukaua simplex Species Araliaceae 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
NPT68 Individual protein Aldose reductase Rattus norvegicus IC50 > 30000.0 nM PMID[22264115]

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 NPC277570 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
0.6744 Remote Similarity NPC233726
0.617 Remote Similarity NPC606861
0.617 Remote Similarity NPC607126
0.5833 Remote Similarity NPC13143
0.5833 Remote Similarity NPC294813
0.5745 Remote Similarity NPC155457
0.5581 Remote Similarity NPC124963
0.5238 Remote Similarity NPC107914
0.5238 Remote Similarity NPC242073
0.5111 Remote Similarity NPC326533

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC277570 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