Natural Product: NPC325443

Natural Product IDNPC325443
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YCZDXXPSFLIESY-MAOFJTBQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 121232717
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000175] Glycerolipids
        • [CHEMONTID:0003815] Triradylcglycerols
          • [CHEMONTID:0001135] Triacylglycerols

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 YCZDXXPSFLIESY-MAOFJTBQSA-N
Standard InCHI InChI=1S/C56H102O6/c1-5-7-9-11-13-15-17-19-21-23-27-31-35-39-43-47-54(57)60-50-53(51-61-55(58)48-44-40-36-32-29-25-26-30-34-38-42-46-52(3)4)62-56(59)49-45-41-37-33-28-24-22-20-18-16-14-12-10-8-6-2/h13,15,19-22,52-53H,5-12,14,16-18,23-51H2,1-4H3/b15-13-,21-19-,22-20-/t53-/m1/s1
SMILES CCCCCCCCC=CCCCCCCCC(=O)OC(COC(=O)CCCCCCCCCCCCCC(C)C)COC(=O)CCCCCCCC=CCC=CCCCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   870.77 Volume:   1014.054
?
Van der Waals volume.
Dense:   0.859 LogP:   11.629
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.718
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -10.67
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   51.0 Rigid Bonds:   6.0
TPSA:   78.9
?
Topological Polar Surface Area.
H-Bond Acceptor:   6.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.026 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.676 Fsp3:   0.839
MCE-18:   5.0
?
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:   0.662 Fluc inhibitor:   0.275
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.0
?
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:   0.785 Promiscuous compounds:   0.299

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.13 MDCK Permeability:   -4.704
Pgp-inhibitor:   0.001 Pgp-substrate:   0.003
PAMPA:   0.0
?
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):   0.528
20% Bioavailability (F20%):   0.999 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   99.739% Volume Distribution (VD):   1.054
Fu: 0.365%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.18
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.657
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.994 CYP2C9-substrate:   0.588
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.354
?
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):  4.344 Half-life (T1/2):  3.113

ADMET: Toxicity

hERG Blockers:  0.918 hERG Blockers (10um):  0.943
Human Hepatotoxicity (H-HT):  0.073 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.324 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.038 Skin Sensitization:  1.0
Carcinogencity:  0.364 Eye Corrosion:  0.893
Eye Irritation:  0.793 Respiratory Toxicity:  0.329
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.093
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.683
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.093
A549 Cytotoxicity:  0.995 Hek293 Cytotoxicity:  0.186
BCF:   -1.626
?
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:   4.559
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.706
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   1.811
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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
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[15690045]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[16529801]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[17558398]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[18650807]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[18791072]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[19346493]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[19549143]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[22235948]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[22239548]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[222395484]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[23163760]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[23475189]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[23894595]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[24411940]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. PMID[24453122]
NPO13691 Caenorhabditis elegans Species Rhabditidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13691 Caenorhabditis elegans Species Rhabditidae 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 NPC325443 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
0.9 High Similarity NPC54925
0.675 Remote Similarity NPC55678
0.6667 Remote Similarity NPC473559
0.6667 Remote Similarity NPC324981
0.6545 Remote Similarity NPC489083
0.6429 Remote Similarity NPC28779
0.6102 Remote Similarity NPC21693
0.6042 Remote Similarity NPC48218
0.6042 Remote Similarity NPC141481
0.6042 Remote Similarity NPC464342
0.5957 Remote Similarity NPC330426
0.5957 Remote Similarity NPC127091
0.5957 Remote Similarity NPC22101
0.5745 Remote Similarity NPC475443
0.5745 Remote Similarity NPC473829
0.5714 Remote Similarity NPC128061
0.5682 Remote Similarity NPC10316
0.5682 Remote Similarity NPC200845
0.5625 Remote Similarity NPC209327
0.5593 Remote Similarity NPC488689
0.5581 Remote Similarity NPC39633
0.5574 Remote Similarity NPC236649
0.5538 Remote Similarity NPC488692
0.5532 Remote Similarity NPC602940
0.551 Remote Similarity NPC273508
0.5455 Remote Similarity NPC470313
0.5455 Remote Similarity NPC473500
0.5455 Remote Similarity NPC611497
0.5417 Remote Similarity NPC321919
0.541 Remote Similarity NPC478995
0.5397 Remote Similarity NPC110813
0.5373 Remote Similarity NPC488691
0.5333 Remote Similarity NPC223677
0.5319 Remote Similarity NPC104537
0.5306 Remote Similarity NPC271921
0.5208 Remote Similarity NPC81896
0.5156 Remote Similarity NPC156089
0.5152 Remote Similarity NPC38295
0.5106 Remote Similarity NPC277597
0.5106 Remote Similarity NPC148192
0.5077 Remote Similarity NPC488694
0.507 Remote Similarity NPC22558

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC325443 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
0.675 Remote Similarity NPD6125 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