Natural Product: NPC167950

Natural Product IDNPC167950
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HEBPYQNXDMDRKR-RYZJKLBQSA-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:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

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 HEBPYQNXDMDRKR-RYZJKLBQSA-N
Standard InCHI InChI=1S/C12H22O8/c1-3-18-8(14)4-6(2)19-12-11(17)10(16)9(15)7(5-13)20-12/h6-7,9-13,15-17H,3-5H2,1-2H3/t6-,7+,9+,10-,11+,12+/m0/s1
SMILES CCOC(=O)C[C@H](C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   294.13 Volume:   275.237
?
Van der Waals volume.
Dense:   1.069 LogP:   -0.562
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.361
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.592
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   7.0
TPSA:   125.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.42 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.82 Fsp3:   0.917
MCE-18:   24.348
?
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:   0.473 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.025
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.403 Promiscuous compounds:   0.036

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.56 MDCK Permeability:   -4.893
Pgp-inhibitor:   0.0 Pgp-substrate:   0.112
PAMPA:   0.982
?
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):   0.021
20% Bioavailability (F20%):   0.05 30% Bioavailability (F30%):   0.355
50% Bioavailability (F50%):   0.919

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.061 MRP1:   0.483
Plasma Protein Binding (PPB):   33.328% Volume Distribution (VD):   -0.531
Fu: 64.376%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.966
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.007
BSEP inhibitor:   0.172

ADMET: Metabolism

CYP1A2-inhibitor:   0.011 CYP1A2-substrate:   0.009
CYP2C19-inhibitor:   0.003 CYP2C19-substrate:   0.123
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.198
CYP3A4-inhibitor:   0.569 CYP3A4-substrate:   0.928
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.977
HLM stability:   0.81
?
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):  2.902 Half-life (T1/2):  2.035

ADMET: Toxicity

hERG Blockers:  0.02 hERG Blockers (10um):  0.105
Human Hepatotoxicity (H-HT):  0.53 Drug-induced Liver Injury (DILI):  0.541
AMES Toxicity:  0.783 Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.033 Skin Sensitization:  0.991
Carcinogencity:  0.369 Eye Corrosion:  0.015
Eye Irritation:  0.676 Respiratory Toxicity:  0.042
Drug-induced Neurotoxicity:  0.065 Ototoxicity:  0.811
Hematotoxicity:  0.365 Drug-induced Nephrotoxicity:  0.679
Genotoxicity:  0.068 RPMI-8226 Immunitoxicity:  0.057
A549 Cytotoxicity:  0.196 Hek293 Cytotoxicity:  0.092
BCF:   0.24
?
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:   1.834
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.157
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.529
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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
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. n.a. n.a. PMID[15743176]
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. Hawaiian n.a. PMID[18407693]
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25777 Acacia longifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26593 Astragalus canadensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26460 Serratia odorifera Species Yersiniaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO12963 Angelica anomala Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26303 Tacca esquirolii Species Taccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25777 Acacia longifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26593 Astragalus canadensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12963 Angelica anomala Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26735 Stevia amambayensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26460 Serratia odorifera Species Yersiniaceae Bacteria 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 NPC167950 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
0.725 Intermediate Similarity NPC268243
0.6316 Remote Similarity NPC124963
0.5789 Remote Similarity NPC23134
0.5682 Remote Similarity NPC155457
0.5581 Remote Similarity NPC233726
0.5366 Remote Similarity NPC326533
0.5294 Remote Similarity NPC206601
0.5185 Remote Similarity NPC482641
0.5128 Remote Similarity NPC42503
0.5128 Remote Similarity NPC282143
0.5128 Remote Similarity NPC107914
0.5128 Remote Similarity NPC242073
0.5128 Remote Similarity NPC299781
0.5128 Remote Similarity NPC157193
0.5128 Remote Similarity NPC608193
0.5106 Remote Similarity NPC13143
0.5106 Remote Similarity NPC294813
0.5106 Remote Similarity NPC603514
0.5106 Remote Similarity NPC606861
0.5106 Remote Similarity NPC607126
0.5102 Remote Similarity NPC482639
0.5094 Remote Similarity NPC471756
0.5094 Remote Similarity NPC12040

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC167950 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
0.5116 Remote Similarity NPD905 Phase 4

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