Natural Product: NPC259317

Natural Product IDNPC259317
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DZTRMTFGDPGXQR-LLGZUXRYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5315586
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 DZTRMTFGDPGXQR-LLGZUXRYSA-N
Standard InCHI InChI=1S/C15H24/c1-10(2)13-8-6-12(4)14-7-5-11(3)9-15(13)14/h6,11,13-15H,1,5,7-9H2,2-4H3/t11-,13?,14?,15-/m0/s1
SMILES C=C(C)C1CC=C(C)C2CC[C@H](C)C[C@@H]12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   204.19 Volume:   245.61
?
Van der Waals volume.
Dense:   0.831 LogP:   4.872
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.615
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.904
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   12.0
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:   4.054 Fsp3:   0.733
MCE-18:   31.385
?
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:   0.217 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.024
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.75 Promiscuous compounds:   0.019

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.785 MDCK Permeability:   -4.675
Pgp-inhibitor:   0.552 Pgp-substrate:   0.025
PAMPA:   0.002
?
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%):   0.009 30% Bioavailability (F30%):   0.047
50% Bioavailability (F50%):   0.529

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.965 MRP1:   0.98
Plasma Protein Binding (PPB):   96.609% Volume Distribution (VD):   0.484
Fu: 3.669%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.972
OATP1B3 inhibitor:   0.991 BCRP inhibitor:   0.626
BSEP inhibitor:   0.919

ADMET: Metabolism

CYP1A2-inhibitor:   0.42 CYP1A2-substrate:   0.921
CYP2C19-inhibitor:   0.992 CYP2C19-substrate:   0.327
CYP2C9-inhibitor:   0.788 CYP2C9-substrate:   0.028
CYP2D6-inhibitor:   0.942 CYP2D6-substrate:   0.376
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   0.987
CYP2B6-substrate:   0.92 CYP2C8-inhibitor:   0.931
HLM stability:   0.862
?
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):  12.348 Half-life (T1/2):  0.984

ADMET: Toxicity

hERG Blockers:  0.054 hERG Blockers (10um):  0.409
Human Hepatotoxicity (H-HT):  0.67 Drug-induced Liver Injury (DILI):  0.434
AMES Toxicity:  0.191 Rat Oral Acute Toxicity:  0.177
Maximum Recommended Daily Dose:  0.428 Skin Sensitization:  0.81
Carcinogencity:  0.77 Eye Corrosion:  0.812
Eye Irritation:  0.952 Respiratory Toxicity:  0.397
Drug-induced Neurotoxicity:  0.644 Ototoxicity:  0.545
Hematotoxicity:  0.279 Drug-induced Nephrotoxicity:  0.3
Genotoxicity:  0.018 RPMI-8226 Immunitoxicity:  0.037
A549 Cytotoxicity:  0.373 Hek293 Cytotoxicity:  0.114
BCF:   2.944
?
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:   4.21
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.051
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.12
?
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
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7635 Glycine max Species Fabaceae 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]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0021-9258(18)90865-3]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1023/A:1024390522259]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15286289]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. seed n.a. PMID[20947202]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24253552]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24954190]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25612070]
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]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36770639]
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]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. stem n.a. Database[Article]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27555 Sedum acre Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Wax n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO18797 Hemibarbus labeo Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27555 Sedum acre Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18797 Hemibarbus labeo Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27555 Sedum acre Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7635 Glycine max Species Fabaceae 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]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27555 Sedum acre Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27555 Sedum acre Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18797 Hemibarbus labeo Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21684 Lathyrus sativus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6701 Cinnamomum camphora Species Lauraceae 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 NPC259317 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
0.5135 Remote Similarity NPC276764
0.5135 Remote Similarity NPC202017

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC259317 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