Natural Product: NPC142713

Natural Product IDNPC142713
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PMLLAVDHHRGJSW-UHFFFAOYSA-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]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0000381] Aporphines

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 PMLLAVDHHRGJSW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H17NO4/c1-20-6-5-10-7-15-19(24-9-23-15)17-11-3-4-14(21)18(22-2)12(11)8-13(20)16(10)17/h3-4,7-8,21H,5-6,9H2,1-2H3
SMILES CN1CCc2cc3c(c4c5ccc(c(c5cc1c24)OC)O)OCO3

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   323.12 Volume:   322.1
?
Van der Waals volume.
Dense:   1.003 LogP:   3.918
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.375
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.752
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   24.0
TPSA:   51.16
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.695 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.868 Fsp3:   0.263
MCE-18:   58.5
?
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:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.911 Fluc inhibitor:   0.052
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.839
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.61
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.006 Promiscuous compounds:   0.261

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.983 MDCK Permeability:   -4.717
Pgp-inhibitor:   0.53 Pgp-substrate:   0.587
PAMPA:   0.068
?
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):   0.105
20% Bioavailability (F20%):   0.183 30% Bioavailability (F30%):   0.11
50% Bioavailability (F50%):   0.689

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.464 MRP1:   0.869
Plasma Protein Binding (PPB):   96.418% Volume Distribution (VD):   0.15
Fu: 3.242%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.794
OATP1B3 inhibitor:   0.732 BCRP inhibitor:   0.391
BSEP inhibitor:   0.789

ADMET: Metabolism

CYP1A2-inhibitor:   0.973 CYP1A2-substrate:   0.494
CYP2C19-inhibitor:   0.932 CYP2C19-substrate:   0.147
CYP2C9-inhibitor:   0.998 CYP2C9-substrate:   0.859
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.989
CYP3A4-inhibitor:   0.126 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.668 CYP2C8-inhibitor:   0.022
HLM stability:   0.589
?
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):  4.452 Half-life (T1/2):  0.995

ADMET: Toxicity

hERG Blockers:  0.44 hERG Blockers (10um):  0.681
Human Hepatotoxicity (H-HT):  0.697 Drug-induced Liver Injury (DILI):  0.843
AMES Toxicity:  0.875 Rat Oral Acute Toxicity:  0.636
Maximum Recommended Daily Dose:  0.785 Skin Sensitization:  0.846
Carcinogencity:  0.9 Eye Corrosion:  0.0
Eye Irritation:  0.59 Respiratory Toxicity:  0.954
Drug-induced Neurotoxicity:  0.813 Ototoxicity:  0.609
Hematotoxicity:  0.676 Drug-induced Nephrotoxicity:  0.775
Genotoxicity:  0.88 RPMI-8226 Immunitoxicity:  0.217
A549 Cytotoxicity:  0.659 Hek293 Cytotoxicity:  0.665
BCF:   1.703
?
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:   4.138
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.897
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.949
?
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
NPO22181 Leibnitzia anandria Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24699147]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota Buds n.a. n.a. PMID[25927817]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[38612781]
NPO20581 Sargassum fulvellum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20965 Oxytropis lanata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7002 Ardisia hortorum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21780 Strychnos gossweileri Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19888 Doronicum grandiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18333 Sphaerophysa salsula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20325 Dictyodendrilla cavernosa Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22181 Leibnitzia anandria Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7002 Ardisia hortorum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7002 Ardisia hortorum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22181 Leibnitzia anandria Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20704 Conus gladiator Species Conidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22498 Lithocarpus haipinii Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19668.1 Euphorbia characias subsp. wulfenii Subspecies Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22181 Leibnitzia anandria Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20581 Sargassum fulvellum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19888 Doronicum grandiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22942 Moesziomyces antarcticus Species Ustilaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22629 Spongia vaginalis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7002 Ardisia hortorum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20965 Oxytropis lanata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22436 Lora quadra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20325 Dictyodendrilla cavernosa Species Dictyodendrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21780 Strychnos gossweileri Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18333 Sphaerophysa salsula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21468 Dilophus guineensis Species Dictyotaceae 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
NPT34 Cell line BV-2 Mus musculus IC50 = 39170.0 nM PMID[37172474]

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 NPC142713 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 NPC611726
0.7097 Intermediate Similarity NPC603719
0.6667 Remote Similarity NPC249405
0.6667 Remote Similarity NPC312531
0.6508 Remote Similarity NPC610105
0.597 Remote Similarity NPC474904
0.5821 Remote Similarity NPC481953
0.5714 Remote Similarity NPC481952
0.5484 Remote Similarity NPC285941
0.5323 Remote Similarity NPC190461

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC142713 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