Natural Product: NPC19470

Natural Product IDNPC19470
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SUXVWSIPTXXPOZ-UXXRCYHCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5316750
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 SUXVWSIPTXXPOZ-UXXRCYHCSA-N
Standard InCHI InChI=1S/C15H20O7/c1-2-3-8-4-5-10(9(17)6-8)21-15-14(20)13(19)12(18)11(7-16)22-15/h2,4-6,11-20H,1,3,7H2/t11-,12-,13+,14-,15-/m1/s1
SMILES C=CCc1ccc(c(c1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   312.12 Volume:   301.869
?
Van der Waals volume.
Dense:   1.034 LogP:   0.288
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.882
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.357
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   119.61
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.456 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.695 Fsp3:   0.467
MCE-18:   48.364
?
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:   0.343 Fluc inhibitor:   0.106
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.032
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.058
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.386 Promiscuous compounds:   0.164

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.794 MDCK Permeability:   -4.98
Pgp-inhibitor:   0.001 Pgp-substrate:   0.0
PAMPA:   0.591
?
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):   0.82
20% Bioavailability (F20%):   0.978 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.028 MRP1:   0.011
Plasma Protein Binding (PPB):   73.506% Volume Distribution (VD):   -0.213
Fu: 25.345%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.323
BSEP inhibitor:   0.017

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.105 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.866 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.104
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.076
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.015
?
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):  3.619 Half-life (T1/2):  2.907

ADMET: Toxicity

hERG Blockers:  0.025 hERG Blockers (10um):  0.212
Human Hepatotoxicity (H-HT):  0.489 Drug-induced Liver Injury (DILI):  0.736
AMES Toxicity:  0.84 Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.02 Skin Sensitization:  0.999
Carcinogencity:  0.251 Eye Corrosion:  0.005
Eye Irritation:  0.67 Respiratory Toxicity:  0.044
Drug-induced Neurotoxicity:  0.027 Ototoxicity:  0.824
Hematotoxicity:  0.154 Drug-induced Nephrotoxicity:  0.428
Genotoxicity:  0.174 RPMI-8226 Immunitoxicity:  0.071
A549 Cytotoxicity:  0.207 Hek293 Cytotoxicity:  0.19
BCF:   0.351
?
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:   2.941
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.417
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.443
?
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
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11908994]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[12016928]
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO32975 ocimum sanctum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17850106]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota stems Ningming County, Guangxi autonomous region, China 2006-Jan PMID[17883259]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. root n.a. PMID[1823989]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[21661731]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[31419126]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31747281]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38791403]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[8594148]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12714 Dracaena cochinchinensis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18983 Cleidion brevipetiolatum Species Euphorbiaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 > 50000.0 nM PMID[31419126]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 3200.0 nM PMID[31747281]

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 NPC19470 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
0.76 Intermediate Similarity NPC60589
0.76 Intermediate Similarity NPC469708
0.7593 Intermediate Similarity NPC210015
0.7037 Intermediate Similarity NPC9912
0.6964 Remote Similarity NPC481303
0.6885 Remote Similarity NPC106944
0.6786 Remote Similarity NPC270849
0.6667 Remote Similarity NPC116229
0.65 Remote Similarity NPC100389
0.6415 Remote Similarity NPC9248
0.6349 Remote Similarity NPC189115
0.6333 Remote Similarity NPC59324
0.629 Remote Similarity NPC186418
0.629 Remote Similarity NPC202700
0.6207 Remote Similarity NPC205054
0.5873 Remote Similarity NPC469661
0.5797 Remote Similarity NPC79957
0.5714 Remote Similarity NPC232228
0.5667 Remote Similarity NPC472024
0.5645 Remote Similarity NPC25292
0.5636 Remote Similarity NPC294470
0.5606 Remote Similarity NPC210192
0.5593 Remote Similarity NPC310661
0.5556 Remote Similarity NPC212729
0.5556 Remote Similarity NPC142319
0.5556 Remote Similarity NPC97326
0.5556 Remote Similarity NPC604498
0.5517 Remote Similarity NPC221090
0.5507 Remote Similarity NPC191046
0.5484 Remote Similarity NPC105827
0.5455 Remote Similarity NPC269242
0.5455 Remote Similarity NPC484157
0.5424 Remote Similarity NPC166168
0.5385 Remote Similarity NPC134260
0.5385 Remote Similarity NPC228907
0.5385 Remote Similarity NPC65530
0.5373 Remote Similarity NPC98777
0.5357 Remote Similarity NPC192810
0.5352 Remote Similarity NPC310064
0.5345 Remote Similarity NPC200092
0.5345 Remote Similarity NPC12308
0.5333 Remote Similarity NPC40377
0.5333 Remote Similarity NPC245615
0.5323 Remote Similarity NPC26653
0.5323 Remote Similarity NPC26080
0.5323 Remote Similarity NPC80600
0.5323 Remote Similarity NPC165686
0.5254 Remote Similarity NPC69513
0.5211 Remote Similarity NPC72249
0.5211 Remote Similarity NPC488085
0.5172 Remote Similarity NPC609376
0.5167 Remote Similarity NPC214454
0.5161 Remote Similarity NPC479769
0.5161 Remote Similarity NPC23084
0.5161 Remote Similarity NPC604356
0.5152 Remote Similarity NPC174377
0.5147 Remote Similarity NPC475096
0.5143 Remote Similarity NPC186406
0.5143 Remote Similarity NPC88043
0.5139 Remote Similarity NPC227902
0.5139 Remote Similarity NPC147596
0.5085 Remote Similarity NPC226712
0.5085 Remote Similarity NPC608788
0.5077 Remote Similarity NPC473045
0.5075 Remote Similarity NPC479374
0.5075 Remote Similarity NPC185778
0.5072 Remote Similarity NPC177742
0.507 Remote Similarity NPC45400
0.5068 Remote Similarity NPC481305
0.5063 Remote Similarity NPC26928

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC19470 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
0.5085 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