Natural Product: NPC246683

Natural Product IDNPC246683
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QVPHNABUSKBIMG-QLCVYAKKSA-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:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives
          • [CHEMONTID:0003002] Hydroxycinnamic acid esters
            • [CHEMONTID:0000465] Coumaric acid esters

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 QVPHNABUSKBIMG-QLCVYAKKSA-N
Standard InCHI InChI=1S/C13H12O7/c14-9-4-1-8(2-5-9)3-6-12(17)20-10(13(18)19)7-11(15)16/h1-6,10,14H,7H2,(H,15,16)(H,18,19)/b6-3+/t10-/m1/s1
SMILES c1cc(ccc1/C=C/C(=O)O[C@H](CC(=O)O)C(=O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   280.06 Volume:   267.924
?
Van der Waals volume.
Dense:   1.045 LogP:   0.993
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.314
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.108
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   10.0
TPSA:   121.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   1.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.522 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.693 Fsp3:   0.154
MCE-18:   18.0
?
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:   0.287 Fluc inhibitor:   0.872
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.179
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.188
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.854 Promiscuous compounds:   0.178

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.334 MDCK Permeability:   -5.178
Pgp-inhibitor:   0.0 Pgp-substrate:   0.0
PAMPA:   0.999
?
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):   0.205
20% Bioavailability (F20%):   0.953 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.052
Plasma Protein Binding (PPB):   79.491% Volume Distribution (VD):   -0.649
Fu: 16.218%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.111

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.441 CYP2C9-substrate:   0.006
CYP2D6-inhibitor:   0.008 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.037
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.989
HLM stability:   0.017
?
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):  4.68 Half-life (T1/2):  1.336

ADMET: Toxicity

hERG Blockers:  0.011 hERG Blockers (10um):  0.02
Human Hepatotoxicity (H-HT):  0.671 Drug-induced Liver Injury (DILI):  0.895
AMES Toxicity:  0.267 Rat Oral Acute Toxicity:  0.108
Maximum Recommended Daily Dose:  0.363 Skin Sensitization:  0.985
Carcinogencity:  0.069 Eye Corrosion:  0.369
Eye Irritation:  0.992 Respiratory Toxicity:  0.048
Drug-induced Neurotoxicity:  0.235 Ototoxicity:  0.3
Hematotoxicity:  0.18 Drug-induced Nephrotoxicity:  0.887
Genotoxicity:  0.843 RPMI-8226 Immunitoxicity:  0.04
A549 Cytotoxicity:  0.001 Hek293 Cytotoxicity:  0.025
BCF:   0.505
?
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:   2.984
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.142
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.776
?
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
NPO8171 Artocarpus altilis Species Moraceae Eukaryota bud covers n.a. n.a. PMID[11975520]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. root n.a. PMID[12662107]
NPO5870 Xenia florida Species n.a. n.a. n.a. n.a. n.a. PMID[16643051]
NPO12386 Russula japonica Species Russulaceae Eukaryota fruiting body n.a. n.a. PMID[16989517]
NPO20045 Burkholderia cepacia Species Burkholderiaceae Bacteria n.a. n.a. n.a. PMID[3839140]
NPO20045 Burkholderia cepacia Species Burkholderiaceae Bacteria n.a. n.a. n.a. PMID[7684040]
NPO5870 Xenia florida Species n.a. n.a. n.a. n.a. n.a. PMID[9868153]
NPO10892 Xanthorrhoea resinosa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20045 Burkholderia cepacia Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO5380 Eucalyptus australiana Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10594 Centaurea solstitialis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14379 Onobrychis viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12386 Russula japonica Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5870 Xenia florida Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO14274 Rhododendron mucronatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7731 Lactuca serriola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14075 Streptomyces viridogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO12726 Piptostigma fugax Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO14274 Rhododendron mucronatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2469 Erythrophleum couminga Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14379 Onobrychis viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7731 Lactuca serriola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7731 Lactuca serriola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14274 Rhododendron mucronatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2469 Erythrophleum couminga Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14379 Onobrychis viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14274 Rhododendron mucronatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2469 Erythrophleum couminga Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8171 Artocarpus altilis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO875 Cryptocarya oblata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12386 Russula japonica Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2469 Erythrophleum couminga Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7608 Phelline lucida Species Phellinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7731 Lactuca serriola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13192 Chara ceratophylla Species Characeae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16013 Inga velutina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12726 Piptostigma fugax Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12035 Rhododendron ungerni Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14274 Rhododendron mucronatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20585 Urochloa decumbens Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16306 Curcuma caesia Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13683 Cosmos diversifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9342 Solenopsis punctaticeps Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO206 Ormosia nobilis Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1398 Trichodesma incanum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11046 Ocimum pilosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5870 Xenia florida Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10892 Xanthorrhoea resinosa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10594 Centaurea solstitialis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5380 Eucalyptus australiana Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20045 Burkholderia cepacia Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12207 Lagochilus leiacanthus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14075 Streptomyces viridogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14379 Onobrychis viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10928 Xenia obscuronata Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3059 Erythrina pallida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2046 Cathormion altissimum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12557 Strychnos tricalysioides Species Loganiaceae 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 NPC246683 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
0.8085 Intermediate Similarity NPC132921
0.6981 Remote Similarity NPC610418
0.6364 Remote Similarity NPC198388
0.6327 Remote Similarity NPC217052
0.6327 Remote Similarity NPC329344
0.6327 Remote Similarity NPC237506
0.6327 Remote Similarity NPC32626
0.625 Remote Similarity NPC108553
0.5926 Remote Similarity NPC251407
0.5926 Remote Similarity NPC168653
0.5833 Remote Similarity NPC156709
0.5778 Remote Similarity NPC253746
0.5574 Remote Similarity NPC279676
0.5439 Remote Similarity NPC18074
0.5439 Remote Similarity NPC5419
0.5439 Remote Similarity NPC25581
0.5439 Remote Similarity NPC61
0.5417 Remote Similarity NPC304638
0.5088 Remote Similarity NPC488563
0.5079 Remote Similarity NPC477333

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC246683 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