Natural Product: NPC168323

Natural Product IDNPC168323
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GFJIQNADMLPFOW-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 547972
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002872] Elemane sesquiterpenoids

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 GFJIQNADMLPFOW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H26O/c1-7-15(6)9-8-12(14(4,5)16)10-13(15)11(2)3/h7,12-13,16H,1-2,8-10H2,3-6H3
SMILES C=CC1(C)CCC(CC1C(=C)C)C(C)(C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   222.2 Volume:   262.957
?
Van der Waals volume.
Dense:   0.845 LogP:   3.461
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.267
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.59
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   8.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.717 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.178 Fsp3:   0.733
MCE-18:   29.538
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.05 Fluc inhibitor:   0.0
?
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:   0.005
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.932 Promiscuous compounds:   0.274

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.878 MDCK Permeability:   -4.761
Pgp-inhibitor:   0.24 Pgp-substrate:   0.001
PAMPA:   0.008
?
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):   0.0
20% Bioavailability (F20%):   0.002 30% Bioavailability (F30%):   0.006
50% Bioavailability (F50%):   0.28

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.97 MRP1:   0.932
Plasma Protein Binding (PPB):   96.754% Volume Distribution (VD):   -0.017
Fu: 3.572%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.365
OATP1B3 inhibitor:   0.954 BCRP inhibitor:   0.861
BSEP inhibitor:   0.476

ADMET: Metabolism

CYP1A2-inhibitor:   0.989 CYP1A2-substrate:   0.277
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.004
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.328
CYP3A4-inhibitor:   0.077 CYP3A4-substrate:   0.256
CYP2B6-substrate:   0.802 CYP2C8-inhibitor:   0.999
HLM stability:   1.0
?
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):  10.985 Half-life (T1/2):  0.921

ADMET: Toxicity

hERG Blockers:  0.04 hERG Blockers (10um):  0.538
Human Hepatotoxicity (H-HT):  0.489 Drug-induced Liver Injury (DILI):  0.134
AMES Toxicity:  0.114 Rat Oral Acute Toxicity:  0.152
Maximum Recommended Daily Dose:  0.396 Skin Sensitization:  0.928
Carcinogencity:  0.751 Eye Corrosion:  0.986
Eye Irritation:  0.997 Respiratory Toxicity:  0.838
Drug-induced Neurotoxicity:  0.562 Ototoxicity:  0.661
Hematotoxicity:  0.246 Drug-induced Nephrotoxicity:  0.056
Genotoxicity:  0.008 RPMI-8226 Immunitoxicity:  0.029
A549 Cytotoxicity:  0.114 Hek293 Cytotoxicity:  0.127
BCF:   1.783
?
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:   3.843
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.407
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.688
?
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
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[10364842]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[12392098]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.49 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.72 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.51 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.54 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.56 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.58 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.57 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.75 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.74 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.52 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.50 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.73 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.47 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.48 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.55 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.53 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.70 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota Seeds Djanga (10.37 N; 4.47 W) and Bérégadougou (10.49 N; 4.76 W) villages in the Southwest of Burkina Faso. PMID[24566330]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24996657]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[25767328]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[33396533]
NPO42048 Rhynchanthus beesianus Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[33997008]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17755 Inula helenium Species Asteraceae 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
NPO42048 Rhynchanthus beesianus Oil n.a. 0.1 n.a. n.a. % PMID[33997008]

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 NPC168323 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
1.0 High Similarity NPC39068
0.6207 Remote Similarity NPC190232
0.6207 Remote Similarity NPC105246
0.5789 Remote Similarity NPC250977
0.5526 Remote Similarity NPC176621
0.5294 Remote Similarity NPC165780
0.5135 Remote Similarity NPC264779
0.5135 Remote Similarity NPC53720
0.5135 Remote Similarity NPC190036
0.5135 Remote Similarity NPC610264

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC168323 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
0.6207 Remote Similarity NPD1799 Clinical (unspecified phase)

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