Natural Product: NPC324810

Natural Product IDNPC324810
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZLJVCXLTFBUWGK-OXGONZEZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 98656794
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 ZLJVCXLTFBUWGK-OXGONZEZSA-N
Standard InCHI InChI=1S/C16H22O8/c1-3-9(18)8-4-5-10(11(6-8)22-2)23-16-15(21)14(20)13(19)12(7-17)24-16/h4-6,12-17,19-21H,3,7H2,1-2H3/t12-,13-,14-,15-,16-/m1/s1
SMILES CCC(=O)C1=CC(=C(C=C1)OC2C(C(C(C(O2)CO)O)O)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   342.13 Volume:   327.955
?
Van der Waals volume.
Dense:   1.043 LogP:   -0.163
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.235
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.54
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   13.0
TPSA:   125.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.508 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.44 Fsp3:   0.562
MCE-18:   51.0
?
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:   0.046 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.037
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.208
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.223 Promiscuous compounds:   0.015

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.661 MDCK Permeability:   -5.061
Pgp-inhibitor:   0.0 Pgp-substrate:   0.752
PAMPA:   0.954
?
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):   0.758
20% Bioavailability (F20%):   0.235 30% Bioavailability (F30%):   0.701
50% Bioavailability (F50%):   0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.07 MRP1:   0.874
Plasma Protein Binding (PPB):   51.669% Volume Distribution (VD):   -0.454
Fu: 48.235%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.001
OATP1B3 inhibitor:   0.576 BCRP inhibitor:   0.407
BSEP inhibitor:   0.673

ADMET: Metabolism

CYP1A2-inhibitor:   0.016 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.029 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.888 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.015 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.027
HLM stability:   0.027
?
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):  3.709 Half-life (T1/2):  1.85

ADMET: Toxicity

hERG Blockers:  0.065 hERG Blockers (10um):  0.429
Human Hepatotoxicity (H-HT):  0.311 Drug-induced Liver Injury (DILI):  0.306
AMES Toxicity:  0.608 Rat Oral Acute Toxicity:  0.332
Maximum Recommended Daily Dose:  0.138 Skin Sensitization:  0.082
Carcinogencity:  0.4 Eye Corrosion:  0.0
Eye Irritation:  0.249 Respiratory Toxicity:  0.495
Drug-induced Neurotoxicity:  0.455 Ototoxicity:  0.774
Hematotoxicity:  0.235 Drug-induced Nephrotoxicity:  0.162
Genotoxicity:  0.169 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.072 Hek293 Cytotoxicity:  0.384
BCF:   0.225
?
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:   2.701
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.398
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.349
?
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
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4340 Peucedanum praeruptorum Species Apiaceae 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 NPC324810 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
0.7143 Intermediate Similarity NPC26653
0.7037 Intermediate Similarity NPC166040
0.6842 Remote Similarity NPC80600
0.6667 Remote Similarity NPC472024
0.6667 Remote Similarity NPC270849
0.6441 Remote Similarity NPC248355
0.6415 Remote Similarity NPC294470
0.6333 Remote Similarity NPC55040
0.623 Remote Similarity NPC302378
0.62 Remote Similarity NPC228907
0.6061 Remote Similarity NPC148273
0.6034 Remote Similarity NPC9912
0.6032 Remote Similarity NPC276753
0.6032 Remote Similarity NPC205796
0.6 Remote Similarity NPC25817
0.5938 Remote Similarity NPC37468
0.5938 Remote Similarity NPC246947
0.5938 Remote Similarity NPC604095
0.5902 Remote Similarity NPC479029
0.5667 Remote Similarity NPC218685
0.5614 Remote Similarity NPC299144
0.5593 Remote Similarity NPC48863
0.5593 Remote Similarity NPC251981
0.5593 Remote Similarity NPC13745
0.5574 Remote Similarity NPC479028
0.5574 Remote Similarity NPC205054
0.5574 Remote Similarity NPC479031
0.5536 Remote Similarity NPC153149
0.5517 Remote Similarity NPC226712
0.55 Remote Similarity NPC215833
0.5493 Remote Similarity NPC227902
0.5455 Remote Similarity NPC276195
0.5455 Remote Similarity NPC486549
0.5455 Remote Similarity NPC212729
0.5455 Remote Similarity NPC604498
0.5429 Remote Similarity NPC158635
0.5429 Remote Similarity NPC229882
0.5424 Remote Similarity NPC69513
0.5357 Remote Similarity NPC217854
0.5357 Remote Similarity NPC269242
0.5352 Remote Similarity NPC61594
0.5352 Remote Similarity NPC286235
0.5345 Remote Similarity NPC609376
0.5323 Remote Similarity NPC23084
0.5294 Remote Similarity NPC475084
0.5278 Remote Similarity NPC38041
0.5278 Remote Similarity NPC18979
0.5278 Remote Similarity NPC22150
0.5278 Remote Similarity NPC279298
0.5278 Remote Similarity NPC56735
0.5254 Remote Similarity NPC200092
0.5254 Remote Similarity NPC608788
0.5238 Remote Similarity NPC210478
0.5205 Remote Similarity NPC471063
0.52 Remote Similarity NPC217635
0.5172 Remote Similarity NPC152722
0.5167 Remote Similarity NPC145900
0.5161 Remote Similarity NPC49074
0.5147 Remote Similarity NPC474044
0.5102 Remote Similarity NPC225245
0.5085 Remote Similarity NPC60589
0.5085 Remote Similarity NPC469708
0.5082 Remote Similarity NPC214454
0.5079 Remote Similarity NPC162093
0.5077 Remote Similarity NPC104167
0.5075 Remote Similarity NPC294166
0.5075 Remote Similarity NPC115022
0.5072 Remote Similarity NPC479450

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC324810 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
0.5517 Remote Similarity NPD1091 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