Natural Product: NPC327049

Natural Product IDNPC327049
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QUOZWMJFTQUXON-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12306788
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 QUOZWMJFTQUXON-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H20O8/c1-7(17)8-3-4-9(10(5-8)21-2)22-15-14(20)13(19)12(18)11(6-16)23-15/h3-5,11-16,18-20H,6H2,1-2H3
SMILES CC(=O)C1=CC(=C(C=C1)OC2C(C(C(C(O2)CO)O)O)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   328.12 Volume:   310.659
?
Van der Waals volume.
Dense:   1.056 LogP:   -0.875
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.366
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.133
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   125.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.511 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.358 Fsp3:   0.533
MCE-18:   51.522
?
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:   0.093 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.031
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.179
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.251 Promiscuous compounds:   0.155

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.662 MDCK Permeability:   -4.938
Pgp-inhibitor:   0.001 Pgp-substrate:   0.671
PAMPA:   0.94
?
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):   0.894
20% Bioavailability (F20%):   0.335 30% Bioavailability (F30%):   0.83
50% Bioavailability (F50%):   0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.097 MRP1:   0.796
Plasma Protein Binding (PPB):   53.966% Volume Distribution (VD):   -0.408
Fu: 45.337%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.008
OATP1B3 inhibitor:   0.926 BCRP inhibitor:   0.126
BSEP inhibitor:   0.091

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.016 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.499 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.005 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.052 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.007
HLM stability:   0.005
?
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):  2.944 Half-life (T1/2):  2.112

ADMET: Toxicity

hERG Blockers:  0.057 hERG Blockers (10um):  0.319
Human Hepatotoxicity (H-HT):  0.557 Drug-induced Liver Injury (DILI):  0.463
AMES Toxicity:  0.628 Rat Oral Acute Toxicity:  0.183
Maximum Recommended Daily Dose:  0.088 Skin Sensitization:  0.212
Carcinogencity:  0.417 Eye Corrosion:  0.0
Eye Irritation:  0.398 Respiratory Toxicity:  0.134
Drug-induced Neurotoxicity:  0.35 Ototoxicity:  0.877
Hematotoxicity:  0.272 Drug-induced Nephrotoxicity:  0.168
Genotoxicity:  0.147 RPMI-8226 Immunitoxicity:  0.095
A549 Cytotoxicity:  0.036 Hek293 Cytotoxicity:  0.232
BCF:   0.176
?
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:   2.262
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.932
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.949
?
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
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jplph.2011.12.019]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1093/jxb/erx356]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. root n.a. PMID[15133218]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. root n.a. PMID[15706916]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[24035096]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[37980871]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10994 Sargentodoxa cuneata Species Lardizabalaceae 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 NPC327049 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
0.7451 Intermediate Similarity NPC166040
0.7358 Intermediate Similarity NPC270849
0.7222 Intermediate Similarity NPC26653
0.7143 Intermediate Similarity NPC294470
0.7037 Intermediate Similarity NPC472024
0.6909 Remote Similarity NPC80600
0.6786 Remote Similarity NPC248355
0.6667 Remote Similarity NPC55040
0.6667 Remote Similarity NPC9912
0.6596 Remote Similarity NPC228907
0.6552 Remote Similarity NPC302378
0.6429 Remote Similarity NPC205054
0.6346 Remote Similarity NPC25817
0.6333 Remote Similarity NPC276753
0.6333 Remote Similarity NPC205796
0.625 Remote Similarity NPC218685
0.623 Remote Similarity NPC37468
0.623 Remote Similarity NPC246947
0.623 Remote Similarity NPC604095
0.6207 Remote Similarity NPC479029
0.5926 Remote Similarity NPC299144
0.5893 Remote Similarity NPC48863
0.5893 Remote Similarity NPC251981
0.5893 Remote Similarity NPC13745
0.5862 Remote Similarity NPC479028
0.5862 Remote Similarity NPC23084
0.5862 Remote Similarity NPC479031
0.5849 Remote Similarity NPC153149
0.5846 Remote Similarity NPC148273
0.5821 Remote Similarity NPC61594
0.5769 Remote Similarity NPC276195
0.5769 Remote Similarity NPC212729
0.5769 Remote Similarity NPC604498
0.5735 Remote Similarity NPC56735
0.5714 Remote Similarity NPC69513
0.5676 Remote Similarity NPC486549
0.5672 Remote Similarity NPC158635
0.5672 Remote Similarity NPC229882
0.566 Remote Similarity NPC217854
0.566 Remote Similarity NPC269242
0.5652 Remote Similarity NPC137813
0.5636 Remote Similarity NPC60589
0.5636 Remote Similarity NPC469708
0.5636 Remote Similarity NPC609376
0.5625 Remote Similarity NPC474044
0.5588 Remote Similarity NPC286235
0.5538 Remote Similarity NPC475084
0.5536 Remote Similarity NPC200092
0.5536 Remote Similarity NPC226712
0.5536 Remote Similarity NPC608788
0.5517 Remote Similarity NPC215833
0.5507 Remote Similarity NPC38041
0.5507 Remote Similarity NPC227902
0.5507 Remote Similarity NPC18979
0.5507 Remote Similarity NPC22150
0.5507 Remote Similarity NPC279298
0.55 Remote Similarity NPC210478
0.5455 Remote Similarity NPC152722
0.5439 Remote Similarity NPC145900
0.5429 Remote Similarity NPC471063
0.5424 Remote Similarity NPC49074
0.5417 Remote Similarity NPC10205
0.5345 Remote Similarity NPC214454
0.5342 Remote Similarity NPC471405
0.5333 Remote Similarity NPC162093
0.5323 Remote Similarity NPC104167
0.5312 Remote Similarity NPC294166
0.5312 Remote Similarity NPC115022
0.5273 Remote Similarity NPC192810
0.527 Remote Similarity NPC186316
0.5238 Remote Similarity NPC247146
0.5238 Remote Similarity NPC604162
0.5231 Remote Similarity NPC479030
0.5224 Remote Similarity NPC178851
0.5205 Remote Similarity NPC93924
0.5205 Remote Similarity NPC217635
0.5195 Remote Similarity NPC476352
0.5185 Remote Similarity NPC142319
0.5172 Remote Similarity NPC221090
0.5172 Remote Similarity NPC80098
0.5152 Remote Similarity NPC146803
0.5152 Remote Similarity NPC216752
0.5135 Remote Similarity NPC43508
0.5132 Remote Similarity NPC478055
0.5085 Remote Similarity NPC95292
0.5082 Remote Similarity NPC19470
0.5082 Remote Similarity NPC604356
0.5079 Remote Similarity NPC95392
0.5079 Remote Similarity NPC84013
0.5079 Remote Similarity NPC222455
0.5079 Remote Similarity NPC55715
0.5079 Remote Similarity NPC35877
0.5077 Remote Similarity NPC96294
0.5075 Remote Similarity NPC210192
0.5075 Remote Similarity NPC475096
0.5072 Remote Similarity NPC212290
0.507 Remote Similarity NPC60249
0.507 Remote Similarity NPC147596
0.5067 Remote Similarity NPC299706
0.5067 Remote Similarity NPC245615
0.5067 Remote Similarity NPC115466
0.5067 Remote Similarity NPC39657
0.5067 Remote Similarity NPC61604
0.5065 Remote Similarity NPC486548

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC327049 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
0.5536 Remote Similarity NPD1091 Pre-clinical

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