Natural Product: NPC261931

Natural Product IDNPC261931
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LKOVPWSSZFDYPG-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 172146
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

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 LKOVPWSSZFDYPG-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h16-17H,2-15H2,1H3,(H,19,20)
SMILES CCCCCCCCCCCCCCCC=CC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   282.26 Volume:   332.192
?
Van der Waals volume.
Dense:   0.85 LogP:   7.121
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.892
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.007
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   2.0
TPSA:   37.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.291 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.012 Fsp3:   0.833
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:   0.485 Fluc inhibitor:   0.172
?
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:   0.021
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.995 Promiscuous compounds:   0.551

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.051 MDCK Permeability:   -4.812
Pgp-inhibitor:   0.0 Pgp-substrate:   0.036
PAMPA:   0.043
?
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):   0.964
20% Bioavailability (F20%):   0.951 30% Bioavailability (F30%):   0.983
50% Bioavailability (F50%):   0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.993
Plasma Protein Binding (PPB):   97.773% Volume Distribution (VD):   0.235
Fu: 1.803%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.382
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.287
BSEP inhibitor:   0.073

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.006
CYP2C19-inhibitor:   0.011 CYP2C19-substrate:   0.021
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.129 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.995
CYP2B6-substrate:   0.236 CYP2C8-inhibitor:   0.954
HLM stability:   0.022
?
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):  3.047 Half-life (T1/2):  1.242

ADMET: Toxicity

hERG Blockers:  0.246 hERG Blockers (10um):  0.475
Human Hepatotoxicity (H-HT):  0.297 Drug-induced Liver Injury (DILI):  0.209
AMES Toxicity:  0.054 Rat Oral Acute Toxicity:  0.271
Maximum Recommended Daily Dose:  0.105 Skin Sensitization:  0.992
Carcinogencity:  0.084 Eye Corrosion:  0.998
Eye Irritation:  0.998 Respiratory Toxicity:  0.904
Drug-induced Neurotoxicity:  0.022 Ototoxicity:  0.222
Hematotoxicity:  0.117 Drug-induced Nephrotoxicity:  0.298
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.025
A549 Cytotoxicity:  0.394 Hek293 Cytotoxicity:  0.047
BCF:   0.813
?
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:   4.265
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.85
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.518
?
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
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. branch n.a. PMID[17202693]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. PMID[38358042]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20554 Astragalus complanatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae 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 NPC261931 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
0.8333 Intermediate Similarity NPC202716
0.75 Intermediate Similarity NPC221250
0.7143 Intermediate Similarity NPC34416
0.5806 Remote Similarity NPC424
0.5806 Remote Similarity NPC36061
0.5806 Remote Similarity NPC69510
0.5806 Remote Similarity NPC77272
0.5806 Remote Similarity NPC290563
0.5806 Remote Similarity NPC139029
0.5806 Remote Similarity NPC281972
0.5806 Remote Similarity NPC261831
0.5806 Remote Similarity NPC87564
0.5625 Remote Similarity NPC95145
0.5625 Remote Similarity NPC325642
0.5625 Remote Similarity NPC65174
0.5517 Remote Similarity NPC118654
0.5484 Remote Similarity NPC281245
0.5357 Remote Similarity NPC171736
0.5357 Remote Similarity NPC301585
0.5357 Remote Similarity NPC261080
0.5357 Remote Similarity NPC132565
0.5357 Remote Similarity NPC209970
0.5357 Remote Similarity NPC216630
0.5357 Remote Similarity NPC201844
0.5357 Remote Similarity NPC301696
0.5357 Remote Similarity NPC196924
0.5357 Remote Similarity NPC307783
0.5357 Remote Similarity NPC154186
0.5357 Remote Similarity NPC149184
0.5357 Remote Similarity NPC279026
0.5357 Remote Similarity NPC113928
0.5357 Remote Similarity NPC14227
0.5312 Remote Similarity NPC92114
0.5294 Remote Similarity NPC154245
0.5294 Remote Similarity NPC85813
0.5294 Remote Similarity NPC223697
0.5294 Remote Similarity NPC6095
0.5278 Remote Similarity NPC487562

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC261931 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
0.5806 Remote Similarity NPD3195 Phase 2
0.5806 Remote Similarity NPD3196 Approved
0.5357 Remote Similarity NPD2270 Pre-clinical
0.5357 Remote Similarity NPD633 Phase 3
0.5357 Remote Similarity NPD9448 Phase 2
0.5294 Remote Similarity NPD4266 Phase 2

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