Natural Product: NPC246783

Natural Product IDNPC246783
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
OREKSZUASHFFQA-DNJKFYBTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 93476678
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

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 OREKSZUASHFFQA-DNJKFYBTSA-N
Standard InCHI InChI=1S/C21H30O5/c1-13-6-9-16-20(2,10-5-11-21(16,3)19(23)24)15(13)8-7-14-12-17(25-4)26-18(14)22/h12,15-17H,1,5-11H2,2-4H3,(H,23,24)/t15-,16+,17-,20+,21-/m0/s1
SMILES C=C1CC[C@@H]2[C@](C)(CCC[C@]2(C)C(=O)O)[C@H]1CCC1=C[C@@H](OC)OC1=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   362.21 Volume:   379.508
?
Van der Waals volume.
Dense:   0.954 LogP:   2.836
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.507
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.878
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   19.0
TPSA:   72.83
?
Topological Polar Surface Area.
H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.589 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.569 Fsp3:   0.714
MCE-18:   56.222
?
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:   0.117 Fluc inhibitor:   0.018
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.03
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.009
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.579 Promiscuous compounds:   0.094

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.757 MDCK Permeability:   -4.832
Pgp-inhibitor:   0.691 Pgp-substrate:   0.0
PAMPA:   0.447
?
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%):   0.127 30% Bioavailability (F30%):   0.103
50% Bioavailability (F50%):   0.186

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.948
Plasma Protein Binding (PPB):   95.277% Volume Distribution (VD):   -0.378
Fu: 3.079%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.988 BCRP inhibitor:   0.001
BSEP inhibitor:   0.993

ADMET: Metabolism

CYP1A2-inhibitor:   0.719 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.099 CYP2C19-substrate:   0.006
CYP2C9-inhibitor:   0.955 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.941 CYP3A4-substrate:   0.006
CYP2B6-substrate:   0.442 CYP2C8-inhibitor:   0.014
HLM stability:   0.188
?
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):  2.882 Half-life (T1/2):  1.126

ADMET: Toxicity

hERG Blockers:  0.031 hERG Blockers (10um):  0.099
Human Hepatotoxicity (H-HT):  0.868 Drug-induced Liver Injury (DILI):  0.827
AMES Toxicity:  0.516 Rat Oral Acute Toxicity:  0.563
Maximum Recommended Daily Dose:  0.718 Skin Sensitization:  0.998
Carcinogencity:  0.715 Eye Corrosion:  0.101
Eye Irritation:  0.87 Respiratory Toxicity:  0.441
Drug-induced Neurotoxicity:  0.584 Ototoxicity:  0.602
Hematotoxicity:  0.267 Drug-induced Nephrotoxicity:  0.984
Genotoxicity:  0.923 RPMI-8226 Immunitoxicity:  0.077
A549 Cytotoxicity:  0.074 Hek293 Cytotoxicity:  0.063
BCF:   0.991
?
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:   4.09
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.595
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.849
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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
NPO17318 Streptomyces cyaneus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21462031]
NPO17158 Trichocereus bridgesii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17318 Streptomyces cyaneus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO25141 Mycetinis alliaceus Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14653 Haliotis diversicolor Species Haliotidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12311 Graphis handelii Species Graphidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15612 Glaucium oxylobum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14339 Fevillea trilobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13361 Clerodendrum tomentosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3705 Anacardium humile Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5124 Aconitum ibukiense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17251 Aniba firmula Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15612 Glaucium oxylobum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15612 Glaucium oxylobum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15612 Glaucium oxylobum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12311 Graphis handelii Species Graphidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5124 Aconitum ibukiense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17318 Streptomyces cyaneus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17158 Trichocereus bridgesii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13361 Clerodendrum tomentosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3705 Anacardium humile Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17251 Aniba firmula Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15612 Glaucium oxylobum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25141 Mycetinis alliaceus Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14339 Fevillea trilobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14653 Haliotis diversicolor Species Haliotidae 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 NPC246783 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
0.7288 Intermediate Similarity NPC600691
0.6935 Remote Similarity NPC477783
0.6833 Remote Similarity NPC40228
0.6379 Remote Similarity NPC481630
0.625 Remote Similarity NPC14203
0.625 Remote Similarity NPC229584
0.625 Remote Similarity NPC477782
0.623 Remote Similarity NPC239098
0.6102 Remote Similarity NPC488498
0.6102 Remote Similarity NPC61952
0.6102 Remote Similarity NPC603184
0.6 Remote Similarity NPC198240
0.6 Remote Similarity NPC72343
0.6 Remote Similarity NPC36616
0.5902 Remote Similarity NPC59436
0.5833 Remote Similarity NPC99154
0.5806 Remote Similarity NPC471159
0.5806 Remote Similarity NPC123880
0.5806 Remote Similarity NPC18819
0.5806 Remote Similarity NPC46610
0.5738 Remote Similarity NPC237591
0.5738 Remote Similarity NPC3753
0.5556 Remote Similarity NPC91369
0.5469 Remote Similarity NPC269543
0.5469 Remote Similarity NPC247783
0.5455 Remote Similarity NPC232344
0.5303 Remote Similarity NPC65661

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC246783 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