Natural Product: NPC152316

Natural Product IDNPC152316
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MAIZBVUEICRYMG-ZIAGYGMSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12097073
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones

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 MAIZBVUEICRYMG-ZIAGYGMSSA-N
Standard InCHI InChI=1S/C15H26O2/c1-11(6-5-9-16)13-10-15(3,4)14(13)8-7-12(2)17/h13-14,16H,1,5-10H2,2-4H3/t13-,14-/m1/s1
SMILES C=C(CCCO)[C@H]1CC(C)(C)[C@@H]1CCC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   238.19 Volume:   271.747
?
Van der Waals volume.
Dense:   0.877 LogP:   2.479
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.248
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.313
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   6.0
TPSA:   37.3
?
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:   0.691 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.972 Fsp3:   0.8
MCE-18:   22.963
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.034 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:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.919 Promiscuous compounds:   0.508

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.872 MDCK Permeability:   -4.715
Pgp-inhibitor:   0.181 Pgp-substrate:   0.127
PAMPA:   0.465
?
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):   0.037
20% Bioavailability (F20%):   0.476 30% Bioavailability (F30%):   0.557
50% Bioavailability (F50%):   0.904

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.788 MRP1:   0.78
Plasma Protein Binding (PPB):   69.859% Volume Distribution (VD):   -0.01
Fu: 29.109%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.662
OATP1B3 inhibitor:   0.937 BCRP inhibitor:   0.123
BSEP inhibitor:   0.128

ADMET: Metabolism

CYP1A2-inhibitor:   0.063 CYP1A2-substrate:   0.172
CYP2C19-inhibitor:   0.835 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.353 CYP2C9-substrate:   0.106
CYP2D6-inhibitor:   0.833 CYP2D6-substrate:   0.043
CYP3A4-inhibitor:   0.014 CYP3A4-substrate:   0.248
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.415
HLM stability:   0.72
?
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):  8.481 Half-life (T1/2):  0.586

ADMET: Toxicity

hERG Blockers:  0.046 hERG Blockers (10um):  0.218
Human Hepatotoxicity (H-HT):  0.445 Drug-induced Liver Injury (DILI):  0.078
AMES Toxicity:  0.133 Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.242 Skin Sensitization:  0.97
Carcinogencity:  0.555 Eye Corrosion:  0.938
Eye Irritation:  0.994 Respiratory Toxicity:  0.749
Drug-induced Neurotoxicity:  0.291 Ototoxicity:  0.496
Hematotoxicity:  0.505 Drug-induced Nephrotoxicity:  0.354
Genotoxicity:  0.007 RPMI-8226 Immunitoxicity:  0.028
A549 Cytotoxicity:  0.004 Hek293 Cytotoxicity:  0.045
BCF:   1.014
?
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:   3.389
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.906
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.08
?
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
NPO2569 Eria yunnanensis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2425 Thunnus obesus Species Scombridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13243 Achillea ligustica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13756 Alpinia conchigera Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10150 Anemone raddeana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15424 Aralia chinensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1386 Bothriocline eupatorioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4388 Gloeophyllum odoratum Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22925 Henriettea fascicularis Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15547 Jaborosa bergii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15099 Machilus parviflora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13381 Pannaria fulvescens Species Pannariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14220 Phoracantha semipunctata Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7879 Plagiochila semidecurrens Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10482 Clitocybe nebularis Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24815 Streptosporangium cinnabarinum Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10150 Anemone raddeana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15424 Aralia chinensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10150 Anemone raddeana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15424 Aralia chinensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4388 Gloeophyllum odoratum Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10150 Anemone raddeana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7879 Plagiochila semidecurrens Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13381 Pannaria fulvescens Species Pannariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15547 Jaborosa bergii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15424 Aralia chinensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15099 Machilus parviflora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10150 Anemone raddeana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13756 Alpinia conchigera Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22925 Henriettea fascicularis Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14220 Phoracantha semipunctata Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1386 Bothriocline eupatorioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4388 Gloeophyllum odoratum Species Gloeophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24815 Streptosporangium cinnabarinum Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2425 Thunnus obesus Species Scombridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13243 Achillea ligustica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2569 Eria yunnanensis Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10482 Clitocybe nebularis Species Tricholomataceae 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 NPC152316 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
0.55 Remote Similarity NPC286752

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC152316 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