Natural Product: NPC327309

Natural Product IDNPC327309
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GQJQCKUJCHMTNF-YBTJCZCISA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 90842945
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 GQJQCKUJCHMTNF-YBTJCZCISA-N
Standard InCHI InChI=1S/C11H20O6/c1-6(2)3-4-16-11-10(15)9(14)8(13)7(5-12)17-11/h3,7-15H,4-5H2,1-2H3/t7-,8-,9+,10-,11?/m1/s1
SMILES CC(=CCOC1C(C(C(C(O1)CO)O)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   248.13 Volume:   240.361
?
Van der Waals volume.
Dense:   1.032 LogP:   -0.473
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.195
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.257
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   7.0
TPSA:   99.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.465 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.775 Fsp3:   0.818
MCE-18:   22.5
?
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:   0.005 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.016
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.005
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.33 Promiscuous compounds:   0.002

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.801 MDCK Permeability:   -5.095
Pgp-inhibitor:   0.001 Pgp-substrate:   0.825
PAMPA:   0.992
?
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):   0.993
20% Bioavailability (F20%):   0.964 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.089 MRP1:   0.855
Plasma Protein Binding (PPB):   34.791% Volume Distribution (VD):   -0.522
Fu: 66.127%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.028
OATP1B3 inhibitor:   0.479 BCRP inhibitor:   0.409
BSEP inhibitor:   0.018

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.674 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.256 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.005 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.406 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.133
HLM stability:   0.036
?
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):  3.606 Half-life (T1/2):  2.0

ADMET: Toxicity

hERG Blockers:  0.046 hERG Blockers (10um):  0.41
Human Hepatotoxicity (H-HT):  0.513 Drug-induced Liver Injury (DILI):  0.326
AMES Toxicity:  0.655 Rat Oral Acute Toxicity:  0.283
Maximum Recommended Daily Dose:  0.071 Skin Sensitization:  0.846
Carcinogencity:  0.347 Eye Corrosion:  0.008
Eye Irritation:  0.694 Respiratory Toxicity:  0.109
Drug-induced Neurotoxicity:  0.415 Ototoxicity:  0.765
Hematotoxicity:  0.179 Drug-induced Nephrotoxicity:  0.109
Genotoxicity:  0.06 RPMI-8226 Immunitoxicity:  0.042
A549 Cytotoxicity:  0.025 Hek293 Cytotoxicity:  0.102
BCF:   0.198
?
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:   1.928
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.466
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.4
?
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
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2008.08.002]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae 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 NPC327309 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
0.7381 Intermediate Similarity NPC63058
0.7059 Intermediate Similarity NPC124963
0.6389 Remote Similarity NPC326533
0.625 Remote Similarity NPC155457
0.6176 Remote Similarity NPC107914
0.6176 Remote Similarity NPC242073
0.6154 Remote Similarity NPC233726
0.6 Remote Similarity NPC23134
0.5952 Remote Similarity NPC13143
0.5952 Remote Similarity NPC294813
0.587 Remote Similarity NPC306255
0.5714 Remote Similarity NPC42503
0.5714 Remote Similarity NPC282143
0.5714 Remote Similarity NPC299781
0.5714 Remote Similarity NPC157193
0.5714 Remote Similarity NPC470124
0.5714 Remote Similarity NPC608193
0.56 Remote Similarity NPC485180
0.5581 Remote Similarity NPC606861
0.5581 Remote Similarity NPC607126
0.551 Remote Similarity NPC313193
0.55 Remote Similarity NPC31496
0.549 Remote Similarity NPC485181
0.5476 Remote Similarity NPC268243
0.54 Remote Similarity NPC9447
0.5385 Remote Similarity NPC137368
0.5349 Remote Similarity NPC145112
0.5319 Remote Similarity NPC147292
0.5263 Remote Similarity NPC603825
0.525 Remote Similarity NPC143326
0.5208 Remote Similarity NPC277570
0.5106 Remote Similarity NPC262826
0.5102 Remote Similarity NPC206601
0.5098 Remote Similarity NPC280367
0.5098 Remote Similarity NPC71381
0.5098 Remote Similarity NPC263407

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC327309 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
0.575 Remote Similarity NPD904 Phase 3

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