Natural Product: NPC115469

Natural Product IDNPC115469
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SATQWIIUJKWZNO-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 529304
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

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 SATQWIIUJKWZNO-UHFFFAOYSA-N
Standard InCHI InChI=1S/C10H18O2/c1-5-10(4,11)7-6-8-9(2,3)12-8/h5,8,11H,1,6-7H2,2-4H3
SMILES C=CC(C)(CCC1C(C)(C)O1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   170.13 Volume:   187.904
?
Van der Waals volume.
Dense:   0.905 LogP:   1.122
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.081
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.685
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   4.0
TPSA:   32.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.516 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.906 Fsp3:   0.8
MCE-18:   22.222
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.001 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.141
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.982 Promiscuous compounds:   0.118

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.794 MDCK Permeability:   -4.791
Pgp-inhibitor:   0.079 Pgp-substrate:   0.172
PAMPA:   0.401
?
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):   0.115
20% Bioavailability (F20%):   0.888 30% Bioavailability (F30%):   0.935
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.103 MRP1:   0.866
Plasma Protein Binding (PPB):   38.234% Volume Distribution (VD):   0.182
Fu: 62.68%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.95
OATP1B3 inhibitor:   0.954 BCRP inhibitor:   0.907
BSEP inhibitor:   0.274

ADMET: Metabolism

CYP1A2-inhibitor:   0.643 CYP1A2-substrate:   0.621
CYP2C19-inhibitor:   0.862 CYP2C19-substrate:   0.019
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.016
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.556
CYP3A4-inhibitor:   0.13 CYP3A4-substrate:   0.034
CYP2B6-substrate:   0.986 CYP2C8-inhibitor:   0.964
HLM stability:   0.856
?
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):  11.222 Half-life (T1/2):  1.476

ADMET: Toxicity

hERG Blockers:  0.076 hERG Blockers (10um):  0.511
Human Hepatotoxicity (H-HT):  0.406 Drug-induced Liver Injury (DILI):  0.123
AMES Toxicity:  0.566 Rat Oral Acute Toxicity:  0.391
Maximum Recommended Daily Dose:  0.313 Skin Sensitization:  0.9
Carcinogencity:  0.662 Eye Corrosion:  0.952
Eye Irritation:  0.988 Respiratory Toxicity:  0.766
Drug-induced Neurotoxicity:  0.503 Ototoxicity:  0.304
Hematotoxicity:  0.251 Drug-induced Nephrotoxicity:  0.193
Genotoxicity:  0.193 RPMI-8226 Immunitoxicity:  0.047
A549 Cytotoxicity:  0.034 Hek293 Cytotoxicity:  0.116
BCF:   0.342
?
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:   2.316
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.825
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.984
?
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
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
NPO19592 Michelia alba Species Magnoliaceae Eukaryota leaves n.a. n.a. PMID[20584613]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24014097]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24128451]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25612070]
NPO13602 Lavandula multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31500359]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[31994661]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32035880]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32674448]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[34500567]
NPO13602 Lavandula multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36676052]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36770639]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[37152127]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[37533252]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[38998569]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[39489989]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. stem n.a. Database[Article]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19592 Michelia alba Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13602 Lavandula multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1479 Amomum longiligulare 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]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19592 Michelia alba Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19592 Michelia alba Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae 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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19592 Michelia alba Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1631 Amomum xanthioides Species Zingiberaceae 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]
NPO1479 Amomum longiligulare Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11820 Amomum villosum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13602 Lavandula multifida Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1631 Amomum xanthioides Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19592 Michelia alba 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
NPO13602 Lavandula multifida Oil n.a. 0.11 n.a. n.a. % PMID[36676052]
NPO6701 Cinnamomum camphora Oil n.a. 0.2 n.a. n.a. % PMID[32035880]
NPO7576 Brassica oleracea Other Stem 0.006 0.006 0.006 mg/100g Database [DUKE]

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 NPC115469 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 NPC115469 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