Natural Product: NPC150465

Natural Product IDNPC150465
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UWSUGXFVYBVFDX-YHYXMXQVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5352146
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 UWSUGXFVYBVFDX-YHYXMXQVSA-N
Standard InCHI InChI=1S/C16H26O/c1-10(9-17)5-4-6-11(2)15-12-7-13-14(8-12)16(13,15)3/h5,11-15,17H,4,6-9H2,1-3H3/b10-5-
SMILES C/C(=C/CCC(C)C1C2CC3C(C2)C13C)/CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   234.2 Volume:   265.777
?
Van der Waals volume.
Dense:   0.881 LogP:   5.111
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.12
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.861
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   10.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.72 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.503 Fsp3:   0.875
MCE-18:   44.4
?
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:   0.018 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.01
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.007
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.645 Promiscuous compounds:   0.266

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.647 MDCK Permeability:   -4.786
Pgp-inhibitor:   0.599 Pgp-substrate:   0.028
PAMPA:   0.006
?
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):   0.042
20% Bioavailability (F20%):   0.02 30% Bioavailability (F30%):   0.303
50% Bioavailability (F50%):   0.675

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.985 MRP1:   0.991
Plasma Protein Binding (PPB):   92.091% Volume Distribution (VD):   0.411
Fu: 8.163%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.001
OATP1B3 inhibitor:   0.08 BCRP inhibitor:   0.163
BSEP inhibitor:   0.976

ADMET: Metabolism

CYP1A2-inhibitor:   0.004 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.995 CYP2C19-substrate:   0.085
CYP2C9-inhibitor:   0.959 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.999 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.994 CYP3A4-substrate:   1.0
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.189
?
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):  15.807 Half-life (T1/2):  1.068

ADMET: Toxicity

hERG Blockers:  0.153 hERG Blockers (10um):  0.493
Human Hepatotoxicity (H-HT):  0.662 Drug-induced Liver Injury (DILI):  0.027
AMES Toxicity:  0.221 Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.298 Skin Sensitization:  0.506
Carcinogencity:  0.291 Eye Corrosion:  0.082
Eye Irritation:  0.921 Respiratory Toxicity:  0.692
Drug-induced Neurotoxicity:  0.286 Ototoxicity:  0.665
Hematotoxicity:  0.114 Drug-induced Nephrotoxicity:  0.175
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.027
A549 Cytotoxicity:  0.035 Hek293 Cytotoxicity:  0.158
BCF:   2.243
?
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:   4.716
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.735
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.379
?
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
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. DOI[10.1016/0045-6535(91)90110-Y]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.abb.2017.09.009]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0885-5765(05)80069-4]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota Roots n.a. n.a. PMID[14510592]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. PMID[15974602]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. exocarp n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. root n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
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]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3572418]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[37152127]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO163 Daucus carota Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17691 Santalum album Species Santalaceae 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]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1479 Amomum longiligulare Species Zingiberaceae 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]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25825 Saussurea lappa 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

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 NPC150465 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 NPC150465 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