Natural Product: NPC10789

Natural Product IDNPC10789
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OSBHLKXCNYMURI-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5321951
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines and derivatives
        • [CHEMONTID:0000056] Quinolones and derivatives
          • [CHEMONTID:0001291] Pyranoquinolines

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 OSBHLKXCNYMURI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H19NO2/c1-12-9-10-15-14(11-12)17-18(23-20(15,2)3)13-7-5-6-8-16(13)21(4)19(17)22/h5-11H,1-4H3
SMILES Cc1ccc2c(-c3c(c4ccccc4n(C)c3=O)OC2(C)C)c1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   305.14 Volume:   327.736
?
Van der Waals volume.
Dense:   0.931 LogP:   3.63
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.322
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.809
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   22.0
TPSA:   31.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   0.0 Rings:   4.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.625 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.515 Fsp3:   0.25
MCE-18:   49.92
?
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:   0.504 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.776
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.542
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.03 Promiscuous compounds:   0.128

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.592 MDCK Permeability:   -4.515
Pgp-inhibitor:   0.853 Pgp-substrate:   0.003
PAMPA:   0.063
?
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%):   0.019
50% Bioavailability (F50%):   0.171

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.577 MRP1:   0.997
Plasma Protein Binding (PPB):   98.562% Volume Distribution (VD):   0.444
Fu: 0.994%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.928
OATP1B3 inhibitor:   0.625 BCRP inhibitor:   0.001
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.725 CYP1A2-substrate:   0.907
CYP2C19-inhibitor:   0.87 CYP2C19-substrate:   0.957
CYP2C9-inhibitor:   0.633 CYP2C9-substrate:   0.029
CYP2D6-inhibitor:   0.068 CYP2D6-substrate:   0.651
CYP3A4-inhibitor:   0.875 CYP3A4-substrate:   0.667
CYP2B6-substrate:   0.53 CYP2C8-inhibitor:   0.791
HLM stability:   0.958
?
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):  3.945 Half-life (T1/2):  0.58

ADMET: Toxicity

hERG Blockers:  0.161 hERG Blockers (10um):  0.56
Human Hepatotoxicity (H-HT):  0.639 Drug-induced Liver Injury (DILI):  0.33
AMES Toxicity:  0.602 Rat Oral Acute Toxicity:  0.461
Maximum Recommended Daily Dose:  0.525 Skin Sensitization:  0.577
Carcinogencity:  0.754 Eye Corrosion:  0.119
Eye Irritation:  0.927 Respiratory Toxicity:  0.733
Drug-induced Neurotoxicity:  0.865 Ototoxicity:  0.389
Hematotoxicity:  0.477 Drug-induced Nephrotoxicity:  0.578
Genotoxicity:  0.397 RPMI-8226 Immunitoxicity:  0.065
A549 Cytotoxicity:  0.143 Hek293 Cytotoxicity:  0.335
BCF:   2.017
?
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:   4.439
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.712
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.398
?
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
NPO26992 Sophora leachiana Species Fabaceae Eukaryota n.a. root n.a. DOI[10.1016/0031-9422(90)85209-X]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. Caribbean n.a. PMID[10021943]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. Taiwan n.a. PMID[11277748]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[15921424]
NPO26203 Dysidea villosa Species Dysideidae Eukaryota n.a. Hainan, China n.a. PMID[19091557]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[23806071]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. China n.a. PMID[25115700]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[26666037]
NPO25406 Celastrus monospermus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[28006915]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[7798955]
NPO25406 Celastrus monospermus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26160 Thielavia terricola Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1267 Acronychia laurifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25802 Agave deserti Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25201 Aglaia pyramidata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25833 Asclepias subulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26203 Dysidea villosa Species Dysideidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3005 Passiflora morifolia Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28636 Vernonia lilacina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26789 Tephrosia bidwilli Species Geometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13313 Talipariti tiliaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26992 Sophora leachiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25714 Solanum spirale Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25358 Senecio gilliesi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25259 Schrebera swietenoides Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22890 Eutrochium purpureum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26849 Parmelia zollingeri Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9324 Notechis scutatus Species Elapidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24478 Morinda coreia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26690 Lactarius subpiperatus Species Lactariidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24918 Jacobaea cannabifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22264 Inula salsoloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19672 Hosta sieboldiana Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24547 Xanthoria parietina Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19672 Hosta sieboldiana Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26992 Sophora leachiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24478 Morinda coreia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13313 Talipariti tiliaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26992 Sophora leachiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24478 Morinda coreia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19672 Hosta sieboldiana Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19672 Hosta sieboldiana Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26298 Zanthoxylum simulans Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24478 Morinda coreia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25201 Aglaia pyramidata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19672 Hosta sieboldiana Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9324 Notechis scutatus Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26160 Thielavia terricola Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26849 Parmelia zollingeri Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25714 Solanum spirale Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25833 Asclepias subulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25406 Celastrus monospermus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26409 Plakortis simplex Species Plakinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24918 Jacobaea cannabifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22890 Eutrochium purpureum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26690 Lactarius subpiperatus Species Lactariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26203 Dysidea villosa Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25802 Agave deserti Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3005 Passiflora morifolia Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26992 Sophora leachiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28636 Vernonia lilacina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25358 Senecio gilliesi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22264 Inula salsoloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25259 Schrebera swietenoides Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24547 Xanthoria parietina Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26789 Tephrosia bidwilli Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1267 Acronychia laurifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13313 Talipariti tiliaceum Species Malvaceae 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 NPC10789 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 NPC10789 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