Natural Product: NPC308809

Natural Product IDNPC308809
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XBGYTZHKGMCEGE-CYKGWVDRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44257927
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001737] Flavonoid C-glycosides
            • [CHEMONTID:0003535] Flavonoid 8-C-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 XBGYTZHKGMCEGE-CYKGWVDRSA-N
Standard InCHI InChI=1S/C26H28O15/c27-5-13-18(33)21(36)23(38)26(41-13)15-19(34)14-10(30)4-12(7-1-2-8(28)9(29)3-7)40-24(14)16(20(15)35)25-22(37)17(32)11(31)6-39-25/h1-4,11,13,17-18,21-23,25-29,31-38H,5-6H2/t11-,13?,17+,18+,21-,22?,23?,25+,26-/m0/s1
SMILES c1cc(c(cc1c1cc(=O)c2c(c(c(c(c2o1)[C@@H]1C([C@@H]([C@H](CO1)O)O)O)O)[C@H]1C([C@H]([C@@H](C(CO)O1)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   580.14 Volume:   526.232
?
Van der Waals volume.
Dense:   1.102 LogP:   -1.266
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.131
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.459
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   30.0
TPSA:   271.2
?
Topological Polar Surface Area.
 H-Bond Acceptor:   15.0
H-Bond Donor:   11.0 Rings:   5.0
Heavy Atoms:   15.0

MedChem Properties

QED Drug-Likeness Score:   0.148 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.863 Fsp3:   0.423
MCE-18:   123.919
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.617 Fluc inhibitor:   0.077
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.836
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.771
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.113 Promiscuous compounds:   0.29

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.486 MDCK Permeability:   -4.996
Pgp-inhibitor:   0.0 Pgp-substrate:   0.873
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):   0.78
20% Bioavailability (F20%):   0.972 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.849
Plasma Protein Binding (PPB):   83.238% Volume Distribution (VD):   0.06
Fu: 14.201%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.291
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.005
BSEP inhibitor:   0.003

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:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.893
HLM stability:   0.105
?
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):  2.35 Half-life (T1/2):  5.369

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.201
Human Hepatotoxicity (H-HT):  0.613 Drug-induced Liver Injury (DILI):  0.834
AMES Toxicity:  0.722 Rat Oral Acute Toxicity:  0.113
Maximum Recommended Daily Dose:  0.4 Skin Sensitization:  0.978
Carcinogencity:  0.037 Eye Corrosion:  0.0
Eye Irritation:  0.169 Respiratory Toxicity:  0.008
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.979
Hematotoxicity:  0.048 Drug-induced Nephrotoxicity:  0.141
Genotoxicity:  0.971 RPMI-8226 Immunitoxicity:  0.088
A549 Cytotoxicity:  0.61 Hek293 Cytotoxicity:  0.379
BCF:   0.387
?
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:   2.822
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.599
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.662
?
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
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11356-018-3422-z]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[15516765]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[20973550]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23700450]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. leaf n.a. PMID[23849114]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24310066]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[25433632]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[26860358]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[38792127]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Protoplast n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae 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 NPC308809 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
0.88 High Similarity NPC326592
0.8312 Intermediate Similarity NPC109594
0.7632 Intermediate Similarity NPC112701
0.6835 Remote Similarity NPC117418
0.675 Remote Similarity NPC53545
0.5904 Remote Similarity NPC209846
0.5833 Remote Similarity NPC328740
0.5833 Remote Similarity NPC289774
0.5806 Remote Similarity NPC218488
0.5732 Remote Similarity NPC477897
0.5714 Remote Similarity NPC289771
0.5326 Remote Similarity NPC111249
0.5312 Remote Similarity NPC607513
0.5243 Remote Similarity NPC482721
0.5189 Remote Similarity NPC324742
0.5055 Remote Similarity NPC10807
0.5055 Remote Similarity NPC161881
0.5052 Remote Similarity NPC47923

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC308809 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