Natural Product: NPC19460

Natural Product IDNPC19460
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VIJZUYWOPTZBJY-HRDQMINSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 91748288
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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 VIJZUYWOPTZBJY-HRDQMINSSA-N
Standard InCHI InChI=1S/C15H24/c1-10(2)13-8-6-12(4)14-7-5-11(3)9-15(13)14/h6,9-11,13-14H,5,7-8H2,1-4H3/t11?,13-,14?/m1/s1
SMILES CC(C)[C@H]1CC=C(C)C2CCC(C)C=C12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   204.19 Volume:   245.61
?
Van der Waals volume.
Dense:   0.831 LogP:   4.969
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.677
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.104
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   11.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.548 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.37 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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.387 Fluc inhibitor:   0.009
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.06
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.026
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.769 Promiscuous compounds:   0.052

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.751 MDCK Permeability:   -4.368
Pgp-inhibitor:   0.996 Pgp-substrate:   0.02
PAMPA:   0.012
?
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):   0.001
20% Bioavailability (F20%):   0.067 30% Bioavailability (F30%):   0.172
50% Bioavailability (F50%):   0.695

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.112 MRP1:   0.982
Plasma Protein Binding (PPB):   97.431% Volume Distribution (VD):   0.228
Fu: 2.519%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.893 BCRP inhibitor:   0.039
BSEP inhibitor:   0.995

ADMET: Metabolism

CYP1A2-inhibitor:   0.126 CYP1A2-substrate:   0.957
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.579
CYP2C9-inhibitor:   0.307 CYP2C9-substrate:   0.025
CYP2D6-inhibitor:   0.133 CYP2D6-substrate:   0.907
CYP3A4-inhibitor:   0.572 CYP3A4-substrate:   0.852
CYP2B6-substrate:   0.958 CYP2C8-inhibitor:   0.957
HLM stability:   0.996
?
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):  9.582 Half-life (T1/2):  0.322

ADMET: Toxicity

hERG Blockers:  0.018 hERG Blockers (10um):  0.299
Human Hepatotoxicity (H-HT):  0.497 Drug-induced Liver Injury (DILI):  0.758
AMES Toxicity:  0.12 Rat Oral Acute Toxicity:  0.484
Maximum Recommended Daily Dose:  0.155 Skin Sensitization:  0.703
Carcinogencity:  0.389 Eye Corrosion:  0.412
Eye Irritation:  0.865 Respiratory Toxicity:  0.577
Drug-induced Neurotoxicity:  0.669 Ototoxicity:  0.413
Hematotoxicity:  0.413 Drug-induced Nephrotoxicity:  0.146
Genotoxicity:  0.08 RPMI-8226 Immunitoxicity:  0.059
A549 Cytotoxicity:  0.153 Hek293 Cytotoxicity:  0.079
BCF:   3.042
?
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:   4.277
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.884
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.069
?
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
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11908994]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. flower bud n.a. PMID[17628872]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. root n.a. PMID[1823989]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[19370929]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[22080044]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO18732 Vetiveria zizanioides Species Poaceae Eukaryota Roots n.a. n.a. PMID[27598828]
NPO18732 Vetiveria zizanioides Species Poaceae Eukaryota n.a. n.a. n.a. PMID[31108854]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31747281]
NPO62378 Cladostephus spongiosus Species Cladostephaceae Eukaryota n.a. n.a. n.a. PMID[37504946]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38791403]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. flower bud n.a. PMID[7779269]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[8594148]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18732 Vetiveria zizanioides Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18732 Vetiveria zizanioides Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25197 Magnolia sprengeri Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18732 Vetiveria zizanioides Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18811 Magnolia biondii Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15064 Magnolia denudata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1918 Magnolia kobus Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15294 Magnolia salicifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25197 Magnolia sprengeri Species Magnoliaceae 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
NPO18732 Vetiveria zizanioides Oil n.a. 4.86 n.a. n.a. % PMID[31108854]
NPO62378 Cladostephus spongiosus Hydro distillation n.a. 0.06 n.a. n.a. % PMID[37504946]

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 NPC19460 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC19460 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