Natural Product: NPC307065

Natural Product IDNPC307065
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VSJBSQHXURXHMK-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6332031
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines and derivatives
        • [CHEMONTID:0001908] Benzoquinolines
          • [CHEMONTID:0000100] Phenanthridines and derivatives

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 VSJBSQHXURXHMK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H15NO4.H2NO3/c1-21-8-15-12(4-5-16-20(15)25-10-22-16)13-3-2-11-6-17-18(24-9-23-17)7-14(11)19(13)21;2-1(3)4/h2-8,11H,9-10H2,1H3;(H2,2,3,4)/q;+1
SMILES CN1C=c2c(=C3C=CC4C=C5C(=CC4=C13)OCO5)ccc1c2OCO1.[N+](=O)(O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   333.1 Volume:   328.203
?
Van der Waals volume.
Dense:   1.015 LogP:   3.005
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.013
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.947
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   29.0
TPSA:   40.16
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   0.0 Rings:   6.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.719 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.601 Fsp3:   0.2
MCE-18:   94.25
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.849 Fluc inhibitor:   0.704
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.835
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.468
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.124 Promiscuous compounds:   0.525

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.92 MDCK Permeability:   -4.671
Pgp-inhibitor:   0.07 Pgp-substrate:   0.12
PAMPA:   0.139
?
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%):   0.012 30% Bioavailability (F30%):   0.001
50% Bioavailability (F50%):   0.365

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.999 MRP1:   0.914
Plasma Protein Binding (PPB):   93.401% Volume Distribution (VD):   0.167
Fu: 7.636%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.635
OATP1B3 inhibitor:   0.556 BCRP inhibitor:   0.004
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.996 CYP1A2-substrate:   0.997
CYP2C19-inhibitor:   0.865 CYP2C19-substrate:   0.362
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   1.0
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.974 CYP2C8-inhibitor:   0.001
HLM stability:   0.994
?
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):  4.619 Half-life (T1/2):  0.618

ADMET: Toxicity

hERG Blockers:  0.37 hERG Blockers (10um):  0.638
Human Hepatotoxicity (H-HT):  0.824 Drug-induced Liver Injury (DILI):  0.977
AMES Toxicity:  0.878 Rat Oral Acute Toxicity:  0.758
Maximum Recommended Daily Dose:  0.912 Skin Sensitization:  0.774
Carcinogencity:  0.926 Eye Corrosion:  0.0
Eye Irritation:  0.467 Respiratory Toxicity:  0.962
Drug-induced Neurotoxicity:  0.926 Ototoxicity:  0.726
Hematotoxicity:  0.703 Drug-induced Nephrotoxicity:  0.768
Genotoxicity:  0.957 RPMI-8226 Immunitoxicity:  0.261
A549 Cytotoxicity:  0.373 Hek293 Cytotoxicity:  0.657
BCF:   1.643
?
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:   4.043
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.756
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.005
?
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
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1042/BA20020118]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1556/abot.45.2003.3-4.15]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[15019787]
NPO6328 Corydalis incisa Species Papaveraceae Eukaryota n.a. aerial part n.a. PMID[17366734]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[21094631]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23517479]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[37685099]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29868 Dicentra spectabilis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28612 Hypecoum leptocarpum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6328 Corydalis incisa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10246 Fumaria officinalis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22043 Hylomecon japonica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28612 Hypecoum leptocarpum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6328 Corydalis incisa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10246 Fumaria officinalis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29868 Dicentra spectabilis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28612 Hypecoum leptocarpum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6328 Corydalis incisa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10246 Fumaria officinalis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22043 Hylomecon japonica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6328 Corydalis incisa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22043 Hylomecon japonica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29868 Dicentra spectabilis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22043 Hylomecon japonica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3504 Argemone mexicana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10246 Fumaria officinalis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6328 Corydalis incisa Species Papaveraceae 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 NPC307065 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC307065 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