Natural Product: NPC221903

Natural Product IDNPC221903
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YPSNWSNUXIIKHO-YANYRWCTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10088114
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 YPSNWSNUXIIKHO-YANYRWCTSA-N
Standard InCHI InChI=1S/C13H16O10/c14-3-7-8(17)9(18)10(19)13(22-7)23-11-5(15)1-4(12(20)21)2-6(11)16/h1-2,7-10,13-19H,3H2,(H,20,21)/t7-,8-,9+,10-,13+/m1/s1
SMILES c1c(cc(c(c1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   332.07 Volume:   293.648
?
Van der Waals volume.
Dense:   1.131 LogP:   -1.1
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.216
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.492
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   13.0
TPSA:   177.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   7.0 Rings:   2.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.325 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.741 Fsp3:   0.462
MCE-18:   56.421
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.269 Fluc inhibitor:   0.123
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.178
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.071
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.436 Promiscuous compounds:   0.901

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.426 MDCK Permeability:   -5.066
Pgp-inhibitor:   0.0 Pgp-substrate:   0.031
PAMPA:   1.0
?
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):   0.066
20% Bioavailability (F20%):   0.036 30% Bioavailability (F30%):   0.361
50% Bioavailability (F50%):   0.314

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.911
Plasma Protein Binding (PPB):   44.668% Volume Distribution (VD):   -0.566
Fu: 59.972%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.992
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.001
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.003
HLM stability:   0.0
?
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):  2.499 Half-life (T1/2):  3.887

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.014
Human Hepatotoxicity (H-HT):  0.685 Drug-induced Liver Injury (DILI):  0.906
AMES Toxicity:  0.637 Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.005 Skin Sensitization:  0.988
Carcinogencity:  0.082 Eye Corrosion:  0.0
Eye Irritation:  0.618 Respiratory Toxicity:  0.016
Drug-induced Neurotoxicity:  0.007 Ototoxicity:  0.957
Hematotoxicity:  0.469 Drug-induced Nephrotoxicity:  0.81
Genotoxicity:  0.255 RPMI-8226 Immunitoxicity:  0.038
A549 Cytotoxicity:  0.032 Hek293 Cytotoxicity:  0.018
BCF:   0.14
?
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:   2.255
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.651
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.125
?
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
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.ecoenv.2016.07.029]
NPO1751 Ribes nigrum Species n.a. n.a. Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. fruit n.a. PMID[16417304]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. fruit n.a. PMID[21648406]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. n.a. PMID[36557810]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[39065796]
NPO22543 Cleome chrysantha Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1751 Ribes nigrum Species n.a. n.a. Fruits n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Seed n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Leaf n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Fruit Juice n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Fruit n.a. n.a. Database[FooDB]
NPO1751 Ribes nigrum Species n.a. n.a. Bulb n.a. n.a. Database[FooDB]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1751 Ribes nigrum Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22543 Cleome chrysantha Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20026 Senecio callosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21977 Psora corallina Species Psoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23380 Camellia japonica Species Theaceae 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
NPO1751 Ribes nigrum Raw n.a. 0.100000004 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO23380 Camellia japonica n.a. Flowers 20.838 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 21.114 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 52.515 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 20.207 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 20.826 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 21.787 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 21.159 n.a. n.a. μg/100g PMID[39065796]
NPO23380 Camellia japonica n.a. Flowers 22.521 n.a. n.a. μg/100g PMID[39065796]
NPO3347 Vaccinium corymbosum Raw n.a. 0.5 n.a. n.a. mg/100g Database [PHENOL EXPLORER]
NPO3347 Vaccinium corymbosum n.a. Fruits 0.5 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]

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 NPC221903 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
0.66 Remote Similarity NPC484157
0.6429 Remote Similarity NPC83975
0.5789 Remote Similarity NPC310661
0.5472 Remote Similarity NPC142319
0.5455 Remote Similarity NPC9248
0.5455 Remote Similarity NPC152722
0.5294 Remote Similarity NPC228907
0.5278 Remote Similarity NPC76112
0.5278 Remote Similarity NPC170018
0.5278 Remote Similarity NPC92403
0.5278 Remote Similarity NPC66820
0.5273 Remote Similarity NPC192810
0.5231 Remote Similarity NPC186418
0.5217 Remote Similarity NPC185103
0.5172 Remote Similarity NPC221090
0.5172 Remote Similarity NPC145900
0.5085 Remote Similarity NPC166168
0.5085 Remote Similarity NPC95292
0.5082 Remote Similarity NPC251102
0.5082 Remote Similarity NPC210298

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC221903 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
0.5278 Remote Similarity NPD8312 Approved
0.5278 Remote Similarity NPD8313 Approved

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