Natural Product: NPC320180

Natural Product IDNPC320180
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RWIINOLFQCPJMH-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 13965334
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 RWIINOLFQCPJMH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H22O9/c1-21-8-3-7(5-16)4-9(22-2)14(8)24-15-13(20)12(19)11(18)10(6-17)23-15/h3-4,10-13,15-20H,5-6H2,1-2H3
SMILES COC1=CC(=CC(=C1OC2C(C(C(C(O2)CO)O)O)O)OC)CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   346.13 Volume:   322.086
?
Van der Waals volume.
Dense:   1.075 LogP:   -1.315
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.692
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.964
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   12.0
TPSA:   138.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   5.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.411 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.522 Fsp3:   0.6
MCE-18:   51.25
?
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:   0.014 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.026
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.252
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.25 Promiscuous compounds:   0.016

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.982 MDCK Permeability:   -5.221
Pgp-inhibitor:   0.0 Pgp-substrate:   0.788
PAMPA:   0.959
?
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):   0.917
20% Bioavailability (F20%):   0.269 30% Bioavailability (F30%):   0.749
50% Bioavailability (F50%):   0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.261 MRP1:   0.8
Plasma Protein Binding (PPB):   53.653% Volume Distribution (VD):   -0.351
Fu: 44.533%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.023
OATP1B3 inhibitor:   0.773 BCRP inhibitor:   0.1
BSEP inhibitor:   0.055

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.731 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.95 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.014 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.836 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.859
HLM stability:   0.0
?
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):  3.43 Half-life (T1/2):  2.424

ADMET: Toxicity

hERG Blockers:  0.036 hERG Blockers (10um):  0.255
Human Hepatotoxicity (H-HT):  0.552 Drug-induced Liver Injury (DILI):  0.256
AMES Toxicity:  0.497 Rat Oral Acute Toxicity:  0.121
Maximum Recommended Daily Dose:  0.101 Skin Sensitization:  0.192
Carcinogencity:  0.446 Eye Corrosion:  0.0
Eye Irritation:  0.216 Respiratory Toxicity:  0.101
Drug-induced Neurotoxicity:  0.491 Ototoxicity:  0.901
Hematotoxicity:  0.169 Drug-induced Nephrotoxicity:  0.198
Genotoxicity:  0.188 RPMI-8226 Immunitoxicity:  0.095
A549 Cytotoxicity:  0.023 Hek293 Cytotoxicity:  0.183
BCF:   0.094
?
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:   1.957
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.449
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.612
?
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
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25577087]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[30827604]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37331322]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2345 Coriandrum sativum 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 NPC320180 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
1.0 High Similarity NPC299144
0.75 Intermediate Similarity NPC69513
0.7347 Intermediate Similarity NPC48863
0.7347 Intermediate Similarity NPC166040
0.7347 Intermediate Similarity NPC251981
0.7347 Intermediate Similarity NPC13745
0.72 Intermediate Similarity NPC215833
0.7174 Intermediate Similarity NPC217854
0.7059 Intermediate Similarity NPC49074
0.6923 Remote Similarity NPC162093
0.6875 Remote Similarity NPC152722
0.6792 Remote Similarity NPC210478
0.6596 Remote Similarity NPC276195
0.6545 Remote Similarity NPC95392
0.6545 Remote Similarity NPC84013
0.6545 Remote Similarity NPC55715
0.6545 Remote Similarity NPC35877
0.6458 Remote Similarity NPC269242
0.6429 Remote Similarity NPC232673
0.6346 Remote Similarity NPC95292
0.6316 Remote Similarity NPC470236
0.6275 Remote Similarity NPC226712
0.6087 Remote Similarity NPC228907
0.6071 Remote Similarity NPC479029
0.6 Remote Similarity NPC153149
0.5962 Remote Similarity NPC608788
0.5926 Remote Similarity NPC40377
0.5882 Remote Similarity NPC25817
0.5833 Remote Similarity NPC479030
0.5818 Remote Similarity NPC218685
0.5806 Remote Similarity NPC216129
0.5806 Remote Similarity NPC130449
0.5806 Remote Similarity NPC248132
0.5714 Remote Similarity NPC472024
0.5714 Remote Similarity NPC479447
0.5714 Remote Similarity NPC270849
0.5714 Remote Similarity NPC605700
0.5686 Remote Similarity NPC192810
0.5614 Remote Similarity NPC26653
0.5614 Remote Similarity NPC80600
0.56 Remote Similarity NPC212729
0.56 Remote Similarity NPC604498
0.5574 Remote Similarity NPC486107
0.5574 Remote Similarity NPC610808
0.5556 Remote Similarity NPC145900
0.5538 Remote Similarity NPC606202
0.5517 Remote Similarity NPC248355
0.5484 Remote Similarity NPC146803
0.5484 Remote Similarity NPC164857
0.5472 Remote Similarity NPC190730
0.5472 Remote Similarity NPC609376
0.5455 Remote Similarity NPC166168
0.5455 Remote Similarity NPC51328
0.5455 Remote Similarity NPC55158
0.5439 Remote Similarity NPC479028
0.5439 Remote Similarity NPC23084
0.5439 Remote Similarity NPC479031
0.5424 Remote Similarity NPC55040
0.5424 Remote Similarity NPC104167
0.5397 Remote Similarity NPC475096
0.5397 Remote Similarity NPC475084
0.5385 Remote Similarity NPC294470
0.537 Remote Similarity NPC12308
0.5357 Remote Similarity NPC310661
0.5357 Remote Similarity NPC9912
0.5345 Remote Similarity NPC164599
0.5333 Remote Similarity NPC302378
0.5312 Remote Similarity NPC485147
0.5294 Remote Similarity NPC199539
0.5294 Remote Similarity NPC142319
0.5273 Remote Similarity NPC221090
0.5238 Remote Similarity NPC604892
0.5231 Remote Similarity NPC486104
0.5231 Remote Similarity NPC486102
0.5192 Remote Similarity NPC484157
0.5185 Remote Similarity NPC60589
0.5185 Remote Similarity NPC469708
0.5172 Remote Similarity NPC606892
0.5161 Remote Similarity NPC276753
0.5161 Remote Similarity NPC205796
0.5156 Remote Similarity NPC210192
0.5143 Remote Similarity NPC605526
0.5091 Remote Similarity NPC200092
0.5082 Remote Similarity NPC34456
0.5079 Remote Similarity NPC37468
0.5079 Remote Similarity NPC246947
0.5079 Remote Similarity NPC604095
0.5075 Remote Similarity NPC212099

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC320180 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
0.6275 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