Natural Product: NPC239479

Natural Product IDNPC239479
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JVAZJLFFSJARQM-SEIUWDOFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 24802191
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 JVAZJLFFSJARQM-SEIUWDOFSA-N
Standard InCHI InChI=1S/C12H24O6/c1-2-3-4-5-6-17-12-11(16)10(15)9(14)8(7-13)18-12/h8-16H,2-7H2,1H3/t8?,9-,10-,11?,12-/m1/s1
SMILES CCCCCCO[C@H]1C([C@@H]([C@@H](C(CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   264.16 Volume:   260.293
?
Van der Waals volume.
Dense:   1.015 LogP:   0.614
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.73
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.244
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   6.0
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:   0.458 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.401 Fsp3:   1.0
MCE-18:   19.333
?
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:   0.095 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.042
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.003
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.369 Promiscuous compounds:   0.004

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.516 MDCK Permeability:   -4.774
Pgp-inhibitor:   0.001 Pgp-substrate:   0.901
PAMPA:   0.978
?
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):   0.944
20% Bioavailability (F20%):   0.865 30% Bioavailability (F30%):   0.976
50% Bioavailability (F50%):   0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.092 MRP1:   0.771
Plasma Protein Binding (PPB):   71.76% Volume Distribution (VD):   -0.181
Fu: 26.58%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.188
OATP1B3 inhibitor:   0.859 BCRP inhibitor:   0.154
BSEP inhibitor:   0.017

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.033
CYP2C19-inhibitor:   0.038 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.214 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.98
HLM stability:   0.007
?
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):  3.727 Half-life (T1/2):  1.707

ADMET: Toxicity

hERG Blockers:  0.122 hERG Blockers (10um):  0.469
Human Hepatotoxicity (H-HT):  0.261 Drug-induced Liver Injury (DILI):  0.054
AMES Toxicity:  0.252 Rat Oral Acute Toxicity:  0.074
Maximum Recommended Daily Dose:  0.015 Skin Sensitization:  0.798
Carcinogencity:  0.139 Eye Corrosion:  0.096
Eye Irritation:  0.75 Respiratory Toxicity:  0.06
Drug-induced Neurotoxicity:  0.02 Ototoxicity:  0.876
Hematotoxicity:  0.158 Drug-induced Nephrotoxicity:  0.167
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.081 Hek293 Cytotoxicity:  0.096
BCF:   0.722
?
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:   3.182
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.648
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.724
?
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
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[17841110]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20778930]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24009 Claviceps purpurea Species Clavicipitaceae 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 NPC239479 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
0.9714 High Similarity NPC606861
0.9714 High Similarity NPC607126
0.8571 High Similarity NPC233726
0.675 Remote Similarity NPC155457
0.6667 Remote Similarity NPC124963
0.6429 Remote Similarity NPC13143
0.6429 Remote Similarity NPC294813
0.6304 Remote Similarity NPC277570
0.6053 Remote Similarity NPC326533
0.5833 Remote Similarity NPC206601
0.5745 Remote Similarity NPC147292
0.5714 Remote Similarity NPC601155
0.5686 Remote Similarity NPC488690
0.5676 Remote Similarity NPC23134
0.56 Remote Similarity NPC12040
0.549 Remote Similarity NPC285003
0.5424 Remote Similarity NPC482018
0.5424 Remote Similarity NPC482015
0.5405 Remote Similarity NPC42503
0.5405 Remote Similarity NPC282143
0.5405 Remote Similarity NPC107914
0.5405 Remote Similarity NPC242073
0.5405 Remote Similarity NPC299781
0.5405 Remote Similarity NPC157193
0.5405 Remote Similarity NPC608193
0.5227 Remote Similarity NPC268243
0.5192 Remote Similarity NPC280367
0.5185 Remote Similarity NPC469469
0.5111 Remote Similarity NPC145112
0.5102 Remote Similarity NPC477750
0.5102 Remote Similarity NPC477763
0.5102 Remote Similarity NPC477757
0.5102 Remote Similarity NPC477762
0.5102 Remote Similarity NPC477755
0.5102 Remote Similarity NPC477753
0.5098 Remote Similarity NPC76881
0.5091 Remote Similarity NPC250619
0.5088 Remote Similarity NPC488689
0.5085 Remote Similarity NPC603467

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC239479 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
0.5476 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