Natural Product: NPC502854

Natural Product IDNPC502854
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 dodec-4-enoic acid
IUPAC Name dodec-4-enoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 GCORITRBZMICMI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C12H22O2/c1-2-3-4-5-6-7-8-9-10-11-12(13)14/h8-9H,2-7,10-11H2,1H3,(H,13,14)
SMILES CCCCCCCC=CCCC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   198.16 Volume:   228.416
?
Van der Waals volume.
Dense:   0.868 LogP:   4.447
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.91
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.501
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 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:   0.452 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.056 Fsp3:   0.75
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.011 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.026
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.866

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.107 MDCK Permeability:   -4.752
Pgp-inhibitor:   0.0 Pgp-substrate:   0.009
PAMPA:   0.616
?
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):   0.055
20% Bioavailability (F20%):   0.051 30% Bioavailability (F30%):   0.1
50% Bioavailability (F50%):   0.066

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.095 MRP1:   0.975
Plasma Protein Binding (PPB):   97.383% Volume Distribution (VD):   -0.077
Fu: 2.249%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.599
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.022
BSEP inhibitor:   0.232

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.715
CYP2C19-inhibitor:   0.023 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.161
CYP2D6-inhibitor:   0.778 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.937
CYP2B6-substrate:   0.968 CYP2C8-inhibitor:   0.902
HLM stability:   0.027
?
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):  4.418 Half-life (T1/2):  0.805

ADMET: Toxicity

hERG Blockers:  0.064 hERG Blockers (10um):  0.233
Human Hepatotoxicity (H-HT):  0.265 Drug-induced Liver Injury (DILI):  0.025
AMES Toxicity:  0.138 Rat Oral Acute Toxicity:  0.115
Maximum Recommended Daily Dose:  0.073 Skin Sensitization:  0.991
Carcinogencity:  0.21 Eye Corrosion:  0.997
Eye Irritation:  0.998 Respiratory Toxicity:  0.669
Drug-induced Neurotoxicity:  0.022 Ototoxicity:  0.214
Hematotoxicity:  0.099 Drug-induced Nephrotoxicity:  0.339
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.032
A549 Cytotoxicity:  0.075 Hek293 Cytotoxicity:  0.035
BCF:   1.129
?
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:   3.789
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.987
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.282
?
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
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. leaf n.a. PMID[17999353]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[18409040]
NPO30603 Saussurea lappa n.a. n.a. n.a. roots n.a. n.a. PMID[18579374]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota Roots; Tubers n.a. n.a. PMID[19639966]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. PMID[25068579]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[8541643]
NPO30115 Aucklandia lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30115 Aucklandia lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4682 Lindera aggregata 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 NPC502854 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
0.7333 Intermediate Similarity NPC424
0.7333 Intermediate Similarity NPC36061
0.7333 Intermediate Similarity NPC69510
0.7333 Intermediate Similarity NPC77272
0.7333 Intermediate Similarity NPC290563
0.7333 Intermediate Similarity NPC139029
0.7333 Intermediate Similarity NPC281972
0.7333 Intermediate Similarity NPC92114
0.7333 Intermediate Similarity NPC261831
0.7333 Intermediate Similarity NPC87564
0.7 Intermediate Similarity NPC281245
0.6667 Remote Similarity NPC154245
0.6667 Remote Similarity NPC85813
0.6667 Remote Similarity NPC223697
0.6667 Remote Similarity NPC59051
0.6667 Remote Similarity NPC6095
0.6562 Remote Similarity NPC95145
0.6562 Remote Similarity NPC325642
0.6562 Remote Similarity NPC65174
0.6364 Remote Similarity NPC321062
0.6364 Remote Similarity NPC91495
0.6364 Remote Similarity NPC5413
0.5946 Remote Similarity NPC52264
0.5806 Remote Similarity NPC270796
0.5714 Remote Similarity NPC52955
0.5714 Remote Similarity NPC88966
0.5714 Remote Similarity NPC25417
0.5714 Remote Similarity NPC1813
0.5676 Remote Similarity NPC137538
0.5641 Remote Similarity NPC477201
0.5526 Remote Similarity NPC487561
0.5429 Remote Similarity NPC70387
0.5366 Remote Similarity NPC243532
0.5333 Remote Similarity NPC171736
0.5333 Remote Similarity NPC301585
0.5333 Remote Similarity NPC261080
0.5333 Remote Similarity NPC132565
0.5333 Remote Similarity NPC209970
0.5333 Remote Similarity NPC216630
0.5333 Remote Similarity NPC201844
0.5333 Remote Similarity NPC301696
0.5333 Remote Similarity NPC196924
0.5333 Remote Similarity NPC307783
0.5333 Remote Similarity NPC154186
0.5333 Remote Similarity NPC149184
0.5333 Remote Similarity NPC279026
0.5333 Remote Similarity NPC113928
0.5333 Remote Similarity NPC14227
0.525 Remote Similarity NPC106851
0.525 Remote Similarity NPC282788
0.525 Remote Similarity NPC274927
0.5238 Remote Similarity NPC68343
0.5238 Remote Similarity NPC328089
0.5143 Remote Similarity NPC149821
0.5128 Remote Similarity NPC606120
0.5122 Remote Similarity NPC179764

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC502854 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
0.7333 Intermediate Similarity NPD3195 Phase 2
0.7333 Intermediate Similarity NPD3196 Approved
0.6842 Remote Similarity NPD39 Phase 4
0.6667 Remote Similarity NPD4266 Phase 2
0.6364 Remote Similarity NPD3173 Phase 4
0.5946 Remote Similarity NPD3194 Phase 4
0.5806 Remote Similarity NPD5326 Phase 3
0.5714 Remote Similarity NPD3172 Approved
0.5429 Remote Similarity NPD3197 Phase 1
0.5333 Remote Similarity NPD2270 Pre-clinical
0.5333 Remote Similarity NPD633 Phase 3
0.5333 Remote Similarity NPD9448 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