Natural Product: NPC218869

Natural Product IDNPC218869
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SNIFAVVHRQZYGO-LUAWRHEFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5353012
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004476] Unsaturated aliphatic hydrocarbons

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 SNIFAVVHRQZYGO-LUAWRHEFSA-N
Standard InCHI InChI=1S/C14H28/c1-3-5-7-9-11-13-14-12-10-8-6-4-2/h9,11H,3-8,10,12-14H2,1-2H3/b11-9-
SMILES CCCC/C=CCCCCCCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   196.22 Volume:   248.064
?
Van der Waals volume.
Dense:   0.791 LogP:   6.961
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.102
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -7.009
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   1.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.32 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.956 Fsp3:   0.857
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:   0.267 Fluc inhibitor:   0.075
?
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:   0.009
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.408

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.001 MDCK Permeability:   -4.743
Pgp-inhibitor:   0.923 Pgp-substrate:   0.001
PAMPA:   0.0
?
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):   0.064
20% Bioavailability (F20%):   0.468 30% Bioavailability (F30%):   0.778
50% Bioavailability (F50%):   0.606

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.536 MRP1:   0.967
Plasma Protein Binding (PPB):   98.247% Volume Distribution (VD):   0.176
Fu: 0.663%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.023
OATP1B3 inhibitor:   0.987 BCRP inhibitor:   0.91
BSEP inhibitor:   0.996

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.007 CYP2C19-substrate:   0.015
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.69
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.823
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.019 CYP2C8-inhibitor:   1.0
HLM stability:   0.139
?
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):  5.845 Half-life (T1/2):  0.425

ADMET: Toxicity

hERG Blockers:  0.521 hERG Blockers (10um):  0.864
Human Hepatotoxicity (H-HT):  0.175 Drug-induced Liver Injury (DILI):  0.001
AMES Toxicity:  0.122 Rat Oral Acute Toxicity:  0.101
Maximum Recommended Daily Dose:  0.134 Skin Sensitization:  1.0
Carcinogencity:  0.067 Eye Corrosion:  0.999
Eye Irritation:  0.998 Respiratory Toxicity:  0.833
Drug-induced Neurotoxicity:  0.014 Ototoxicity:  0.097
Hematotoxicity:  0.014 Drug-induced Nephrotoxicity:  0.293
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.064
A549 Cytotoxicity:  0.921 Hek293 Cytotoxicity:  0.449
BCF:   2.311
?
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:   4.947
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.002
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.516
?
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
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36838931]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37480748]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae 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 NPC218869 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
1.0 High Similarity NPC151719
0.6842 Remote Similarity NPC182392
0.65 Remote Similarity NPC44363
0.65 Remote Similarity NPC125129
0.65 Remote Similarity NPC110234
0.65 Remote Similarity NPC76976
0.65 Remote Similarity NPC163751
0.625 Remote Similarity NPC266539
0.625 Remote Similarity NPC179103
0.625 Remote Similarity NPC88325
0.625 Remote Similarity NPC287191
0.625 Remote Similarity NPC31891
0.625 Remote Similarity NPC266144
0.625 Remote Similarity NPC76765
0.6 Remote Similarity NPC34671
0.6 Remote Similarity NPC11487
0.6 Remote Similarity NPC67920
0.6 Remote Similarity NPC239754
0.6 Remote Similarity NPC252978
0.6 Remote Similarity NPC33489
0.6 Remote Similarity NPC298710
0.6 Remote Similarity NPC311716
0.6 Remote Similarity NPC217923
0.6 Remote Similarity NPC287397
0.5909 Remote Similarity NPC261571
0.5909 Remote Similarity NPC188341
0.55 Remote Similarity NPC33761
0.5417 Remote Similarity NPC474642
0.5417 Remote Similarity NPC473913
0.5417 Remote Similarity NPC309606
0.5385 Remote Similarity NPC273385
0.5385 Remote Similarity NPC278711
0.5385 Remote Similarity NPC98925
0.5385 Remote Similarity NPC64370
0.5385 Remote Similarity NPC82648
0.5385 Remote Similarity NPC227986
0.5385 Remote Similarity NPC239406
0.5385 Remote Similarity NPC77249
0.5385 Remote Similarity NPC26974
0.5385 Remote Similarity NPC136996
0.5385 Remote Similarity NPC302327
0.5385 Remote Similarity NPC154477
0.5385 Remote Similarity NPC89422
0.5385 Remote Similarity NPC26229
0.5333 Remote Similarity NPC178306
0.5217 Remote Similarity NPC15934
0.5217 Remote Similarity NPC155880
0.5217 Remote Similarity NPC609384
0.52 Remote Similarity NPC49494
0.52 Remote Similarity NPC262968
0.52 Remote Similarity NPC600749
0.52 Remote Similarity NPC601019

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC218869 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
0.52 Remote Similarity NPD28 Approved
0.52 Remote Similarity NPD29 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