Natural Product: NPC295389

Natural Product IDNPC295389
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
6-O-Palmitoyl-Beta-D-Glucosyl-Beta-Sitosterol
IUPAC Name [(2R,3S,4S,5R,6R)-6-[[(3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5S)-5-ethyl-6-methylheptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]-3,4,5-trihydroxyoxan-2-yl]methyl hexadecanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL499385
PubChem CID 44593507
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002031] Stigmastanes and derivatives

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 JCLYMCVRBRHEHI-FLBTYZGGSA-N
Standard InCHI InChI=1S/C51H90O7/c1-8-10-11-12-13-14-15-16-17-18-19-20-21-22-45(52)56-34-44-46(53)47(54)48(55)49(58-44)57-39-29-31-50(6)38(33-39)25-26-40-42-28-27-41(51(42,7)32-30-43(40)50)36(5)23-24-37(9-2)35(3)4/h25,35-37,39-44,46-49,53-55H,8-24,26-34H2,1-7H3/t36-,37+,39+,40+,41-,42+,43+,44-,46-,47+,48-,49-,50+,51-/m1/s1
SMILES CCCCCCCCCCCCCCCC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](O[C@H]2CC[C@@]3(C)C(=CC[C@H]4[C@@H]5CC[C@H]([C@H](C)CC[C@H](CC)C(C)C)[C@@]5(C)CC[C@H]34)C2)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   814.67 Volume:   904.128
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Van der Waals volume.
Dense:   0.901 LogP:   12.684
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   7.122
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -8.451
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The logarithm of aqueous solubility value.
Rotatable Bonds:   25.0 Rigid Bonds:   27.0
TPSA:   105.45
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Topological Polar Surface Area.
H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   5.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.051 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.303 Fsp3:   0.941
MCE-18:   86.545
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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:   0 PAINS Alert:   0
Colloidal aggregators:   0.999 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.26 Promiscuous compounds:   0.013

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.388 MDCK Permeability:   -4.802
Pgp-inhibitor:   0.002 Pgp-substrate:   0.051
PAMPA:   0.009
?
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):   0.002
20% Bioavailability (F20%):   0.825 30% Bioavailability (F30%):   0.993
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.568
Plasma Protein Binding (PPB):   98.563% Volume Distribution (VD):   0.569
Fu: 1.103%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.544
BSEP inhibitor:   0.943

ADMET: Metabolism

CYP1A2-inhibitor:   0.008 CYP1A2-substrate:   0.783
CYP2C19-inhibitor:   0.761 CYP2C19-substrate:   0.996
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.058
CYP3A4-inhibitor:   0.985 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.868
?
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):  2.83 Half-life (T1/2):  2.055

ADMET: Toxicity

hERG Blockers:  0.334 hERG Blockers (10um):  0.65
Human Hepatotoxicity (H-HT):  0.432 Drug-induced Liver Injury (DILI):  0.868
AMES Toxicity:  0.113 Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.071 Skin Sensitization:  1.0
Carcinogencity:  0.281 Eye Corrosion:  0.002
Eye Irritation:  0.185 Respiratory Toxicity:  0.664
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.821
Hematotoxicity:  0.305 Drug-induced Nephrotoxicity:  0.953
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.104
A549 Cytotoxicity:  0.976 Hek293 Cytotoxicity:  0.467
BCF:   1.475
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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:   5.991
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.018
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   7.093
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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
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11473446]
NPO33450 aplinia officinarum Species n.a. n.a. n.a. n.a. n.a. PMID[12350154]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Fruits n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22234 Ficus carica Species Moraceae 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
NPT673 Organism Gallus gallus Gallus gallus Inhibition = 50.9 % PMID[19928902]





 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 NPC295389 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
0.7215 Intermediate Similarity NPC22140
0.7215 Intermediate Similarity NPC243728
0.6477 Remote Similarity NPC486114
0.5897 Remote Similarity NPC44083
0.5814 Remote Similarity NPC158088
0.5814 Remote Similarity NPC21064
0.5783 Remote Similarity NPC207617
0.5783 Remote Similarity NPC607440
0.5581 Remote Similarity NPC473890
0.5568 Remote Similarity NPC470434
0.5506 Remote Similarity NPC282669
0.5333 Remote Similarity NPC608180
0.5287 Remote Similarity NPC264127
0.5258 Remote Similarity NPC272015
0.5169 Remote Similarity NPC121072
0.5104 Remote Similarity NPC220048
0.5104 Remote Similarity NPC251614

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC295389 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