Natural Product: NPC289206

Natural Product IDNPC289206
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HXLZULGRVFOIDK-AVQMFFATSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5283383
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000298] Fatty aldehydes

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 HXLZULGRVFOIDK-AVQMFFATSA-N
Standard InCHI InChI=1S/C18H32O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19/h6-7,9-10,18H,2-5,8,11-17H2,1H3/b7-6+,10-9+
SMILES CCCCC/C=C/C/C=C/CCCCCCCC=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   264.25 Volume:   320.765
?
Van der Waals volume.
Dense:   0.824 LogP:   5.892
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.636
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.659
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   3.0
TPSA:   17.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.214 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.505 Fsp3:   0.722
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:   0.6 Fluc inhibitor:   0.086
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.016
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.401

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.038 MDCK Permeability:   -4.735
Pgp-inhibitor:   0.589 Pgp-substrate:   0.007
PAMPA:   0.0
?
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):   0.003
20% Bioavailability (F20%):   0.166 30% Bioavailability (F30%):   0.404
50% Bioavailability (F50%):   0.894

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.88
Plasma Protein Binding (PPB):   98.515% Volume Distribution (VD):   -0.191
Fu: 0.594%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.122
OATP1B3 inhibitor:   0.981 BCRP inhibitor:   0.224
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.885
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.605
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.994
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.185 CYP2C8-inhibitor:   1.0
HLM stability:   0.623
?
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):  5.969 Half-life (T1/2):  0.387

ADMET: Toxicity

hERG Blockers:  0.222 hERG Blockers (10um):  0.697
Human Hepatotoxicity (H-HT):  0.873 Drug-induced Liver Injury (DILI):  0.367
AMES Toxicity:  0.011 Rat Oral Acute Toxicity:  0.085
Maximum Recommended Daily Dose:  0.174 Skin Sensitization:  0.999
Carcinogencity:  0.034 Eye Corrosion:  0.088
Eye Irritation:  0.923 Respiratory Toxicity:  0.967
Drug-induced Neurotoxicity:  0.184 Ototoxicity:  0.467
Hematotoxicity:  0.278 Drug-induced Nephrotoxicity:  0.435
Genotoxicity:  0.012 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.15 Hek293 Cytotoxicity:  0.127
BCF:   1.627
?
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:   4.987
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.174
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.127
?
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
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[26521454]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[32872604]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[36352904]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[39679248]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[39680258]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18951 Ligusticum sinense Species Apiaceae 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 NPC289206 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
0.8696 High Similarity NPC44363
0.8696 High Similarity NPC110234
0.8696 High Similarity NPC163751
0.8261 Intermediate Similarity NPC11487
0.8261 Intermediate Similarity NPC239754
0.6154 Remote Similarity NPC67920
0.6154 Remote Similarity NPC33489
0.6154 Remote Similarity NPC298710
0.6154 Remote Similarity NPC311716
0.6154 Remote Similarity NPC287397
0.6087 Remote Similarity NPC32279
0.6087 Remote Similarity NPC265705
0.6087 Remote Similarity NPC262505
0.6087 Remote Similarity NPC179831
0.6087 Remote Similarity NPC261991
0.6087 Remote Similarity NPC49615
0.6087 Remote Similarity NPC49151
0.6087 Remote Similarity NPC254713
0.6071 Remote Similarity NPC155880
0.5769 Remote Similarity NPC33761
0.5652 Remote Similarity NPC151719
0.5652 Remote Similarity NPC59581
0.5625 Remote Similarity NPC39633
0.5625 Remote Similarity NPC477458
0.5556 Remote Similarity NPC34671
0.5357 Remote Similarity NPC125129
0.5294 Remote Similarity NPC154245
0.5294 Remote Similarity NPC85813
0.5294 Remote Similarity NPC223697
0.5294 Remote Similarity NPC59051
0.5294 Remote Similarity NPC28779
0.5294 Remote Similarity NPC6095
0.5172 Remote Similarity NPC208936

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC289206 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
0.5294 Remote Similarity NPD4266 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