Natural Product: NPC207254

Natural Product IDNPC207254
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OOAFRMHKOSBPID-HIFRSBDPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 46848746
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000027] Indanes
        • [CHEMONTID:0001151] Indanones

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 OOAFRMHKOSBPID-HIFRSBDPSA-N
Standard InCHI InChI=1S/C15H20O4/c1-8-6-11-12(9(2)10(8)4-5-16)14(19)15(3,7-17)13(11)18/h6,13,16-18H,4-5,7H2,1-3H3/t13-,15+/m1/s1
SMILES Cc1cc2c(c(C)c1CCO)C(=O)[C@@](C)(CO)[C@@H]2O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   264.14 Volume:   275.498
?
Van der Waals volume.
Dense:   0.959 LogP:   1.167
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.603
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.469
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   11.0
TPSA:   77.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.763 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.857 Fsp3:   0.533
MCE-18:   50.783
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.026 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.37
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.051
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.224 Promiscuous compounds:   0.088

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.844 MDCK Permeability:   -4.677
Pgp-inhibitor:   0.113 Pgp-substrate:   0.778
PAMPA:   0.997
?
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%):   0.013 30% Bioavailability (F30%):   0.004
50% Bioavailability (F50%):   0.393

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.811 MRP1:   0.98
Plasma Protein Binding (PPB):   64.92% Volume Distribution (VD):   0.072
Fu: 39.079%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.951
OATP1B3 inhibitor:   0.304 BCRP inhibitor:   0.125
BSEP inhibitor:   0.973

ADMET: Metabolism

CYP1A2-inhibitor:   0.014 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.36 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.03
CYP3A4-inhibitor:   0.23 CYP3A4-substrate:   0.167
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.003
HLM stability:   0.006
?
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):  7.138 Half-life (T1/2):  1.716

ADMET: Toxicity

hERG Blockers:  0.033 hERG Blockers (10um):  0.137
Human Hepatotoxicity (H-HT):  0.834 Drug-induced Liver Injury (DILI):  0.491
AMES Toxicity:  0.759 Rat Oral Acute Toxicity:  0.197
Maximum Recommended Daily Dose:  0.163 Skin Sensitization:  0.993
Carcinogencity:  0.891 Eye Corrosion:  0.005
Eye Irritation:  0.865 Respiratory Toxicity:  0.295
Drug-induced Neurotoxicity:  0.138 Ototoxicity:  0.7
Hematotoxicity:  0.71 Drug-induced Nephrotoxicity:  0.801
Genotoxicity:  0.292 RPMI-8226 Immunitoxicity:  0.136
A549 Cytotoxicity:  0.282 Hek293 Cytotoxicity:  0.288
BCF:   0.493
?
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:   3.105
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.51
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.702
?
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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[10978200]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1776 Attalea excelsa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1776 Attalea excelsa Species Arecaceae 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 NPC207254 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 NPC31499
0.7857 Intermediate Similarity NPC46971
0.7805 Intermediate Similarity NPC22531
0.587 Remote Similarity NPC135654
0.587 Remote Similarity NPC269860
0.587 Remote Similarity NPC190729
0.587 Remote Similarity NPC485143
0.5652 Remote Similarity NPC112903
0.5106 Remote Similarity NPC83409

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC207254 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