Natural Product: NPC327389

Natural Product IDNPC327389
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
OUHLKPMNPWFJMR-VAODPLLESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 121232714
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 OUHLKPMNPWFJMR-VAODPLLESA-N
Standard InCHI InChI=1S/C53H100O6/c1-5-7-9-11-13-15-17-19-20-21-25-29-33-37-41-45-52(55)58-48-50(47-57-51(54)44-40-36-32-28-24-18-16-14-12-10-8-6-2)59-53(56)46-42-38-34-30-26-22-23-27-31-35-39-43-49(3)4/h19-20,49-50H,5-18,21-48H2,1-4H3/b20-19-/t50-/m0/s1
SMILES CCCCCCCCCCCCCCC(=O)OCC(COC(=O)CCCCCCCC=CCCCCCCCC)OC(=O)CCCCCCCCCCCCCC(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   832.75 Volume:   967.439
?
Van der Waals volume.
Dense:   0.861 LogP:   7.072
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.031
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -6.907
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   50.0 Rigid Bonds:   4.0
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:   3.39 Fsp3:   0.906
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:   0.657 Fluc inhibitor:   0.315
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.0
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.004
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.875 Promiscuous compounds:   0.218

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.2 MDCK Permeability:   -4.867
Pgp-inhibitor:   0.0 Pgp-substrate:   0.01
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):   0.968
20% Bioavailability (F20%):   1.0 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):   101.747% Volume Distribution (VD):   1.91
Fu: 0.207%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.133
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.876
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.991
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.153 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.049
?
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):  4.27 Half-life (T1/2):  4.246

ADMET: Toxicity

hERG Blockers:  0.934 hERG Blockers (10um):  0.966
Human Hepatotoxicity (H-HT):  0.317 Drug-induced Liver Injury (DILI):  0.018
AMES Toxicity:  0.156 Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.109 Skin Sensitization:  1.0
Carcinogencity:  0.67 Eye Corrosion:  0.498
Eye Irritation:  0.66 Respiratory Toxicity:  0.703
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.137
Hematotoxicity:  0.014 Drug-induced Nephrotoxicity:  0.685
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.107
A549 Cytotoxicity:  0.996 Hek293 Cytotoxicity:  0.256
BCF:   -1.737
?
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:   4.506
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.641
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   1.784
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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 NPC327389 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
0.825 Intermediate Similarity NPC54925
0.7297 Intermediate Similarity NPC55678
0.6444 Remote Similarity NPC48218
0.6444 Remote Similarity NPC141481
0.6444 Remote Similarity NPC464342
0.6154 Remote Similarity NPC128061
0.6042 Remote Similarity NPC473559
0.6042 Remote Similarity NPC324981
0.6 Remote Similarity NPC209327
0.6 Remote Similarity NPC489083
0.5909 Remote Similarity NPC602940
0.5893 Remote Similarity NPC488689
0.587 Remote Similarity NPC273508
0.5714 Remote Similarity NPC223677
0.5714 Remote Similarity NPC28779
0.569 Remote Similarity NPC478995
0.5682 Remote Similarity NPC104537
0.5593 Remote Similarity NPC21693
0.5455 Remote Similarity NPC277597
0.5455 Remote Similarity NPC148192
0.541 Remote Similarity NPC156089
0.5323 Remote Similarity NPC488694
0.5319 Remote Similarity NPC330426
0.5319 Remote Similarity NPC127091
0.5319 Remote Similarity NPC22101
0.525 Remote Similarity NPC309606
0.5192 Remote Similarity NPC224700
0.5192 Remote Similarity NPC320663
0.5106 Remote Similarity NPC475443
0.5106 Remote Similarity NPC473829
0.5082 Remote Similarity NPC236649
0.5077 Remote Similarity NPC488692

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC327389 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
0.7297 Intermediate Similarity NPD6125 Phase 4
0.5192 Remote Similarity NPD8278 Phase 4
0.5111 Remote Similarity NPD3730 Pre-clinical

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