Natural Product: NPC158339

Natural Product IDNPC158339
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IGGWKHQYMAJOHK-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 518574
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 IGGWKHQYMAJOHK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H34O/c1-7-18(4)13-9-16-19(5)12-8-11-17(2,3)15(19)10-14-20(16,6)21-18/h7,15-16H,1,8-14H2,2-6H3
SMILES C=CC1(C)CCC2C3(C)CCCC(C)(C)C3CCC2(C)O1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.26 Volume:   334.961
?
Van der Waals volume.
Dense:   0.867 LogP:   4.526
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.6
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.874
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   9.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.559 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.307 Fsp3:   0.9
MCE-18:   61.737
?
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.121 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.017
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.971 Promiscuous compounds:   0.069

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.812 MDCK Permeability:   -4.785
Pgp-inhibitor:   0.132 Pgp-substrate:   0.0
PAMPA:   0.003
?
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%):   0.0 30% Bioavailability (F30%):   0.0
50% Bioavailability (F50%):   0.263

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   1.0 MRP1:   0.991
Plasma Protein Binding (PPB):   98.44% Volume Distribution (VD):   0.721
Fu: 1.922%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.007
OATP1B3 inhibitor:   0.818 BCRP inhibitor:   0.012
BSEP inhibitor:   0.901

ADMET: Metabolism

CYP1A2-inhibitor:   0.956 CYP1A2-substrate:   0.918
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.353
CYP2C9-inhibitor:   0.996 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.994 CYP2D6-substrate:   0.045
CYP3A4-inhibitor:   0.409 CYP3A4-substrate:   1.0
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   0.969
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):  12.319 Half-life (T1/2):  0.74

ADMET: Toxicity

hERG Blockers:  0.119 hERG Blockers (10um):  0.832
Human Hepatotoxicity (H-HT):  0.307 Drug-induced Liver Injury (DILI):  0.204
AMES Toxicity:  0.082 Rat Oral Acute Toxicity:  0.143
Maximum Recommended Daily Dose:  0.526 Skin Sensitization:  0.965
Carcinogencity:  0.546 Eye Corrosion:  0.998
Eye Irritation:  0.997 Respiratory Toxicity:  0.851
Drug-induced Neurotoxicity:  0.655 Ototoxicity:  0.612
Hematotoxicity:  0.135 Drug-induced Nephrotoxicity:  0.051
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.054
A549 Cytotoxicity:  0.155 Hek293 Cytotoxicity:  0.169
BCF:   2.646
?
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:   5.007
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.268
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.496
?
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
NPO57214 Cupressus lusitanica Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[ 11339951]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[10606602]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22264035]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[31475763]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[35268681]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36031812]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36671701]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36982252]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36987013]
NPO26268 Salvia aethiopis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36987013]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37299156]
NPO57214 Cupressus lusitanica Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[37482262]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37836125]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37960139]
NPO23682 Juniperus phoenicea Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[38263385]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38308284]
NPO21065 Euphorbia calyptrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[38528316]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38606448]
NPO26268 Salvia aethiopis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38611827]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38611827]
NPO53768 Salvia ringens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38611827]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38802729]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39147955]
NPO23682 Juniperus phoenicea Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[39345860]
NPO55822 Kleinia anteuphorbium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39403475]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[39410132]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39599440]
NPO23682 Juniperus phoenicea Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[6253598]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23682 Juniperus phoenicea Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26268 Salvia aethiopis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO57214 Cupressus lusitanica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23682 Juniperus phoenicea Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21065 Euphorbia calyptrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1439 Mentha longifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26268 Salvia aethiopis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7317 Citrus aurantium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14822 Salvia sclarea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23682 Juniperus phoenicea Species Cupressaceae 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
NPO1439 Mentha longifolia Oil Seeds 0.21 n.a. n.a. % PMID[36031812]
NPO14822 Salvia sclarea Oil n.a. 0.2 n.a. n.a. % PMID[38611827]
NPO14822 Salvia sclarea Oil n.a. 0.3 n.a. n.a. % PMID[38611827]
NPO18735 Pinus mugo Oil n.a. 0.3 n.a. n.a. % PMID[31475763]
NPO18735 Pinus mugo Oil n.a. 0.2 n.a. n.a. % PMID[31475763]
NPO21065 Euphorbia calyptrata Oil n.a. 2.02 n.a. n.a. % PMID[38528316]
NPO23682 Juniperus phoenicea Oil n.a. 0.95 n.a. n.a. % PMID[39345860]
NPO26268 Salvia aethiopis Oil n.a. 0.4 n.a. n.a. % PMID[38611827]
NPO53768 Salvia ringens Oil n.a. 0.1 n.a. n.a. % PMID[38611827]
NPO55822 Kleinia anteuphorbium Oil n.a. 0.22 n.a. n.a. % PMID[39403475]
NPO57214 Cupressus lusitanica Oil n.a. 0.59 n.a. n.a. % PMID[37482262]

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 NPC158339 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 NPC42630
0.7209 Intermediate Similarity NPC137587
0.6444 Remote Similarity NPC479669
0.6222 Remote Similarity NPC198473
0.5957 Remote Similarity NPC479670
0.5778 Remote Similarity NPC139785
0.5682 Remote Similarity NPC607221
0.5556 Remote Similarity NPC84562
0.5556 Remote Similarity NPC608369
0.549 Remote Similarity NPC20096
0.549 Remote Similarity NPC48673
0.5439 Remote Similarity NPC289361
0.52 Remote Similarity NPC72755
0.52 Remote Similarity NPC476367

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC158339 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