Natural Product: NPC484321

Natural Product IDNPC484321
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZIHVXDPAMALUML-PZBSJLNOSA-N
IUPAC Name n.a.
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 ZIHVXDPAMALUML-PZBSJLNOSA-N
Standard InCHI InChI=1S/C20H28O4/c1-3-19(22)14-10-7-8-12-16-20(23)15-11-6-4-5-9-13-17-24-18(2)21/h3,12,16,19-20,22-23H,1,4-6,9,11,13,15,17H2,2H3/b16-12+/t19-,20+/m1/s1
SMILES C=C[C@H](C#CC#C/C=C/[C@H](CCCCCCCCOC(=O)C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   332.2 Volume:   371.182
?
Van der Waals volume.
Dense:   0.895 LogP:   3.134
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.631
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.466
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   5.0
TPSA:   66.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.264 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.977 Fsp3:   0.55
MCE-18:   3.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.17 Fluc inhibitor:   0.059
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.016
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.662 Promiscuous compounds:   0.235

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.787 MDCK Permeability:   -4.629
Pgp-inhibitor:   0.002 Pgp-substrate:   0.0
PAMPA:   0.999
?
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%):   0.0 30% Bioavailability (F30%):   0.004
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   80.217% Volume Distribution (VD):   0.013
Fu: 9.977%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.004 BCRP inhibitor:   1.0
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.041
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.101
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.598
CYP3A4-inhibitor:   0.011 CYP3A4-substrate:   0.033
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.993
?
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):  4.094 Half-life (T1/2):  1.251

ADMET: Toxicity

hERG Blockers:  0.087 hERG Blockers (10um):  0.596
Human Hepatotoxicity (H-HT):  0.341 Drug-induced Liver Injury (DILI):  0.364
AMES Toxicity:  0.241 Rat Oral Acute Toxicity:  0.229
Maximum Recommended Daily Dose:  0.409 Skin Sensitization:  0.59
Carcinogencity:  0.595 Eye Corrosion:  0.866
Eye Irritation:  0.991 Respiratory Toxicity:  0.969
Drug-induced Neurotoxicity:  0.225 Ototoxicity:  0.366
Hematotoxicity:  0.036 Drug-induced Nephrotoxicity:  0.093
Genotoxicity:  0.007 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.037 Hek293 Cytotoxicity:  0.169
BCF:   1.193
?
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:   4.18
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.785
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.227
?
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
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[20218656]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota Tubers n.a. n.a. PMID[23356207]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[9392889]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25695 Oplopanax horridus Species Araliaceae 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
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens FC = 1.0 n.a. PMID[32129622]

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 NPC484321 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
0.6818 Remote Similarity NPC49059
0.6818 Remote Similarity NPC481849
0.6818 Remote Similarity NPC201681
0.6809 Remote Similarity NPC66460
0.6809 Remote Similarity NPC325929
0.6809 Remote Similarity NPC271282
0.6522 Remote Similarity NPC480799
0.6444 Remote Similarity NPC481848
0.6222 Remote Similarity NPC481855
0.5962 Remote Similarity NPC484323
0.5686 Remote Similarity NPC29697
0.5435 Remote Similarity NPC484322
0.5306 Remote Similarity NPC481856
0.52 Remote Similarity NPC35602
0.5102 Remote Similarity NPC481857
0.5091 Remote Similarity NPC265551
0.5091 Remote Similarity NPC472445
0.5091 Remote Similarity NPC481635

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484321 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