Natural Product: NPC295904

Natural Product IDNPC295904
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 TYEPJNKESLRTEJ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 549045
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000504] Lineolic acids and derivatives

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 TYEPJNKESLRTEJ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H34O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19(20)21-2/h6-7,9-10H,3-5,8,11-18H2,1-2H3
SMILES CCCCC=CCC=CCCCCCCCCC(=O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   294.26 Volume:   346.851
?
Van der Waals volume.
Dense:   0.848 LogP:   6.848
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.989
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.474
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   3.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.224 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.337 Fsp3:   0.737
MCE-18:   0.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.226 Fluc inhibitor:   0.251
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.015
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.995 Promiscuous compounds:   0.507

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.992 MDCK Permeability:   -4.738
Pgp-inhibitor:   0.164 Pgp-substrate:   0.057
PAMPA:   0.005
?
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):   0.026
20% Bioavailability (F20%):   0.309 30% Bioavailability (F30%):   0.617
50% Bioavailability (F50%):   0.722

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.086 MRP1:   0.991
Plasma Protein Binding (PPB):   98.039% Volume Distribution (VD):   -0.38
Fu: 1.491%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.117
OATP1B3 inhibitor:   0.989 BCRP inhibitor:   0.67
BSEP inhibitor:   0.979

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.18 CYP2C19-substrate:   0.914
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.041
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.997
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.97 CYP2C8-inhibitor:   1.0
HLM stability:   0.997
?
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):  5.815 Half-life (T1/2):  0.306

ADMET: Toxicity

hERG Blockers:  0.241 hERG Blockers (10um):  0.619
Human Hepatotoxicity (H-HT):  0.113 Drug-induced Liver Injury (DILI):  0.002
AMES Toxicity:  0.225 Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.093 Skin Sensitization:  1.0
Carcinogencity:  0.237 Eye Corrosion:  0.998
Eye Irritation:  0.998 Respiratory Toxicity:  0.568
Drug-induced Neurotoxicity:  0.016 Ototoxicity:  0.137
Hematotoxicity:  0.019 Drug-induced Nephrotoxicity:  0.309
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.11 Hek293 Cytotoxicity:  0.032
BCF:   1.444
?
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:   4.553
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.959
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.511
?
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
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19270100148]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Petals n.a. n.a. PMID[15043425]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24338885]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[34771092]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[37111302]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38786901]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae 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 NPC295904 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
0.963 High Similarity NPC39633
0.8929 High Similarity NPC139545
0.8519 High Similarity NPC309606
0.7333 Intermediate Similarity NPC228473
0.7188 Intermediate Similarity NPC28779
0.6667 Remote Similarity NPC10316
0.6667 Remote Similarity NPC200845
0.6296 Remote Similarity NPC201622
0.6296 Remote Similarity NPC305660
0.6296 Remote Similarity NPC161097
0.6296 Remote Similarity NPC28598
0.6296 Remote Similarity NPC22903
0.6296 Remote Similarity NPC54980
0.625 Remote Similarity NPC128061
0.6216 Remote Similarity NPC475443
0.6216 Remote Similarity NPC473829
0.6207 Remote Similarity NPC216130
0.6053 Remote Similarity NPC330426
0.6053 Remote Similarity NPC127091
0.6053 Remote Similarity NPC22101
0.5897 Remote Similarity NPC54925
0.5769 Remote Similarity NPC219536
0.5769 Remote Similarity NPC31551
0.5714 Remote Similarity NPC223677
0.5641 Remote Similarity NPC271921
0.5556 Remote Similarity NPC476548
0.5526 Remote Similarity NPC81896
0.5405 Remote Similarity NPC277597
0.5405 Remote Similarity NPC148192
0.5385 Remote Similarity NPC321919
0.5385 Remote Similarity NPC57499
0.5349 Remote Similarity NPC473559
0.5349 Remote Similarity NPC324981
0.5263 Remote Similarity NPC104537
0.5238 Remote Similarity NPC473772
0.5143 Remote Similarity NPC71761

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC295904 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
0.5588 Remote Similarity NPD5343 Phase 4
0.5278 Remote Similarity NPD6096 Phase 4

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