Natural Product: NPC324659

Natural Product IDNPC324659
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SNOSCANYFCXCGY-UPHRSURJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 56928100
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000504] Lineolic acids and derivatives

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 SNOSCANYFCXCGY-UPHRSURJSA-N
Standard InCHI InChI=1S/C18H32O3/c19-17-15-13-11-9-7-5-3-1-2-4-6-8-10-12-14-16-18(20)21/h1-2,17H,3-16H2,(H,20,21)/b2-1-
SMILES C(CCCC=CCCCCCCCC(=O)O)CCCC=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   296.24 Volume:   338.345
?
Van der Waals volume.
Dense:   0.876 LogP:   5.104
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.855
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.184
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   3.0
TPSA:   54.37
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.239 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.298 Fsp3:   0.778
MCE-18:   0.0
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.075 Fluc inhibitor:   0.069
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
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:   0.992 Promiscuous compounds:   0.819

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.081 MDCK Permeability:   -4.713
Pgp-inhibitor:   0.0 Pgp-substrate:   0.008
PAMPA:   0.174
?
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):   0.683
20% Bioavailability (F20%):   0.523 30% Bioavailability (F30%):   0.864
50% Bioavailability (F50%):   0.367

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.959
Plasma Protein Binding (PPB):   96.987% Volume Distribution (VD):   -0.44
Fu: 2.719%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.134
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.083
BSEP inhibitor:   0.584

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.993
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.129
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.02
CYP2D6-inhibitor:   0.731 CYP2D6-substrate:   0.007
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.266 CYP2C8-inhibitor:   1.0
HLM stability:   0.001
?
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):  3.642 Half-life (T1/2):  0.791

ADMET: Toxicity

hERG Blockers:  0.068 hERG Blockers (10um):  0.118
Human Hepatotoxicity (H-HT):  0.192 Drug-induced Liver Injury (DILI):  0.022
AMES Toxicity:  0.075 Rat Oral Acute Toxicity:  0.05
Maximum Recommended Daily Dose:  0.073 Skin Sensitization:  1.0
Carcinogencity:  0.06 Eye Corrosion:  0.998
Eye Irritation:  0.998 Respiratory Toxicity:  0.743
Drug-induced Neurotoxicity:  0.007 Ototoxicity:  0.224
Hematotoxicity:  0.061 Drug-induced Nephrotoxicity:  0.526
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.019
A549 Cytotoxicity:  0.012 Hek293 Cytotoxicity:  0.013
BCF:   1.096
?
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:   4.124
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.57
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.034
?
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]
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]
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]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
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]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
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. seed n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7635 Glycine max Species Fabaceae Eukaryota 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 Testa n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem 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 Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling 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 Oil 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 Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit 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 n.a. n.a. Database[FooDB]
NPO7635 Glycine max 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]
NPO7635 Glycine max 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]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7635 Glycine max Species Fabaceae 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 NPC324659 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
0.7667 Intermediate Similarity NPC281245
0.7419 Intermediate Similarity NPC424
0.7419 Intermediate Similarity NPC36061
0.7419 Intermediate Similarity NPC69510
0.7419 Intermediate Similarity NPC77272
0.7419 Intermediate Similarity NPC290563
0.7419 Intermediate Similarity NPC139029
0.7419 Intermediate Similarity NPC281972
0.7419 Intermediate Similarity NPC261831
0.7419 Intermediate Similarity NPC87564
0.6875 Remote Similarity NPC92114
0.6765 Remote Similarity NPC52955
0.6765 Remote Similarity NPC88966
0.6765 Remote Similarity NPC25417
0.6765 Remote Similarity NPC1813
0.6765 Remote Similarity NPC154245
0.6765 Remote Similarity NPC85813
0.6765 Remote Similarity NPC223697
0.6765 Remote Similarity NPC6095
0.6667 Remote Similarity NPC95145
0.6667 Remote Similarity NPC325642
0.6667 Remote Similarity NPC65174
0.6471 Remote Similarity NPC321062
0.6471 Remote Similarity NPC70387
0.6452 Remote Similarity NPC180534
0.6452 Remote Similarity NPC611531
0.6154 Remote Similarity NPC477201
0.6071 Remote Similarity NPC214610
0.6071 Remote Similarity NPC118968
0.6071 Remote Similarity NPC183424
0.6071 Remote Similarity NPC294085
0.6061 Remote Similarity NPC34416
0.6053 Remote Similarity NPC606120
0.6 Remote Similarity NPC5413
0.5833 Remote Similarity NPC59051
0.575 Remote Similarity NPC106851
0.575 Remote Similarity NPC282788
0.575 Remote Similarity NPC274927
0.5714 Remote Similarity NPC149821
0.5714 Remote Similarity NPC268826
0.5714 Remote Similarity NPC207292
0.5667 Remote Similarity NPC11487
0.5667 Remote Similarity NPC239754
0.5641 Remote Similarity NPC225929
0.5556 Remote Similarity NPC91495
0.5484 Remote Similarity NPC171736
0.5484 Remote Similarity NPC301585
0.5484 Remote Similarity NPC44363
0.5484 Remote Similarity NPC261080
0.5484 Remote Similarity NPC110234
0.5484 Remote Similarity NPC132565
0.5484 Remote Similarity NPC209970
0.5484 Remote Similarity NPC216630
0.5484 Remote Similarity NPC201844
0.5484 Remote Similarity NPC301696
0.5484 Remote Similarity NPC163751
0.5484 Remote Similarity NPC196924
0.5484 Remote Similarity NPC307783
0.5484 Remote Similarity NPC154186
0.5484 Remote Similarity NPC149184
0.5484 Remote Similarity NPC279026
0.5484 Remote Similarity NPC113928
0.5484 Remote Similarity NPC14227
0.5476 Remote Similarity NPC251042
0.5476 Remote Similarity NPC243532
0.5476 Remote Similarity NPC174447
0.5476 Remote Similarity NPC122521
0.5405 Remote Similarity NPC174560
0.5405 Remote Similarity NPC125312
0.5349 Remote Similarity NPC68343
0.5349 Remote Similarity NPC328089
0.5312 Remote Similarity NPC604140
0.5238 Remote Similarity NPC179764
0.5172 Remote Similarity NPC134782
0.5161 Remote Similarity NPC155263
0.5135 Remote Similarity NPC48162
0.5116 Remote Similarity NPC255863
0.5116 Remote Similarity NPC473863
0.5116 Remote Similarity NPC136164
0.5116 Remote Similarity NPC245947

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC324659 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
0.7419 Intermediate Similarity NPD3195 Phase 2
0.7419 Intermediate Similarity NPD3196 Approved
0.6765 Remote Similarity NPD3172 Approved
0.6765 Remote Similarity NPD4266 Phase 2
0.6452 Remote Similarity NPD622 Pre-clinical
0.6071 Remote Similarity NPD9655 Phase 4
0.6053 Remote Similarity NPD3194 Phase 4
0.6 Remote Similarity NPD3173 Phase 4
0.5484 Remote Similarity NPD2270 Pre-clinical
0.5484 Remote Similarity NPD633 Phase 3
0.5484 Remote Similarity NPD9448 Phase 2
0.5349 Remote Similarity NPD39 Phase 4

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