Natural Product: NPC473150

Natural Product IDNPC473150
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CAFTUQNGDROXEZ-NINKYYIQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3622809
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0004081] Iridoid O-glycosides

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 CAFTUQNGDROXEZ-NINKYYIQSA-N
Standard InCHI InChI=1S/C17H26O11/c1-7(19)28-16(2)5-9(20)17(24)3-4-25-15(13(16)17)27-14-12(23)11(22)10(21)8(6-18)26-14/h3-4,8-15,18,20-24H,5-6H2,1-2H3/t8-,9-,10-,11+,12-,13-,14+,15+,16-,17-/m1/s1
SMILES CC(=O)OC1(CC(C2(C1C(OC=C2)OC3C(C(C(C(O3)CO)O)O)O)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   406.15 Volume:   368.338
?
Van der Waals volume.
Dense:   1.103 LogP:   -1.966
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.191
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.332
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   17.0
TPSA:   175.37
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   6.0 Rings:   3.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.264 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.97 Fsp3:   0.824
MCE-18:   65.032
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.004 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.034
?
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:   0.368 Promiscuous compounds:   0.023

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.03 MDCK Permeability:   -5.058
Pgp-inhibitor:   0.0 Pgp-substrate:   0.977
PAMPA:   1.0
?
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):   0.993
20% Bioavailability (F20%):   0.941 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.017 MRP1:   0.946
Plasma Protein Binding (PPB):   23.37% Volume Distribution (VD):   -0.671
Fu: 84.945%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.002
OATP1B3 inhibitor:   0.501 BCRP inhibitor:   0.058
BSEP inhibitor:   0.005

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.01 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.612 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.005
HLM stability:   0.0
?
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):  1.264 Half-life (T1/2):  2.759

ADMET: Toxicity

hERG Blockers:  0.024 hERG Blockers (10um):  0.279
Human Hepatotoxicity (H-HT):  0.459 Drug-induced Liver Injury (DILI):  0.614
AMES Toxicity:  0.88 Rat Oral Acute Toxicity:  0.359
Maximum Recommended Daily Dose:  0.237 Skin Sensitization:  0.69
Carcinogencity:  0.456 Eye Corrosion:  0.0
Eye Irritation:  0.024 Respiratory Toxicity:  0.018
Drug-induced Neurotoxicity:  0.632 Ototoxicity:  0.948
Hematotoxicity:  0.062 Drug-induced Nephrotoxicity:  0.277
Genotoxicity:  0.675 RPMI-8226 Immunitoxicity:  0.085
A549 Cytotoxicity:  0.027 Hek293 Cytotoxicity:  0.249
BCF:   0.141
?
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:   2.057
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.967
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.922
?
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
NPO33356 vitex mollis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[26351040]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26351040]
NPO33113 castilleja tenuiflora Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[26351040]
NPO33328 cresentia alata Species n.a. n.a. n.a. n.a. n.a. PMID[26351040]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33113 castilleja tenuiflora Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33328 cresentia alata Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO33356 vitex mollis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20005 Penstemon barbatus Species Plantaginaceae 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
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens Inhibition = 38.5 % PMID[16643022]
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens Inhibition = 38.6 % PMID[16643022]
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens Inhibition = 39.1 % PMID[16643022]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens Inhibition = 37.3 % PMID[23668986]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens Inhibition = 37.7 % PMID[23668986]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens Inhibition = 38.8 % PMID[23668986]

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 NPC473150 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 NPC274274
1.0 High Similarity NPC294643
0.7143 Intermediate Similarity NPC276047
0.7143 Intermediate Similarity NPC267733
0.7049 Intermediate Similarity NPC93190
0.6944 Remote Similarity NPC49597
0.6757 Remote Similarity NPC263397
0.6757 Remote Similarity NPC88754
0.6271 Remote Similarity NPC171484
0.6271 Remote Similarity NPC149018
0.623 Remote Similarity NPC151308
0.619 Remote Similarity NPC50464
0.5595 Remote Similarity NPC481006

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473150 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