Natural Product: NPC248743

Natural Product IDNPC248743
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AJLVEHFNMNRXNI-VMQOHUEUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
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:0002207] O-glycosyl compounds

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 AJLVEHFNMNRXNI-VMQOHUEUSA-N
Standard InCHI InChI=1S/C9H18O7/c1-4(11)3-15-9-8(14)7(13)6(12)5(2-10)16-9/h4-14H,2-3H2,1H3/t4-,5-,6-,7+,8-,9-/m1/s1
SMILES C[C@H](CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   238.11 Volume:   217.195
?
Van der Waals volume.
Dense:   1.096 LogP:   -1.743
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.23
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.096
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   6.0
TPSA:   119.61
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   1.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.358 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.797 Fsp3:   1.0
MCE-18:   23.0
?
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:   0.258 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.041
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.428 Promiscuous compounds:   0.008

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.045 MDCK Permeability:   -4.955
Pgp-inhibitor:   0.0 Pgp-substrate:   0.285
PAMPA:   0.99
?
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):   0.463
20% Bioavailability (F20%):   0.148 30% Bioavailability (F30%):   0.92
50% Bioavailability (F50%):   0.863

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.014 MRP1:   0.075
Plasma Protein Binding (PPB):   29.096% Volume Distribution (VD):   -0.583
Fu: 78.181%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.056
BSEP inhibitor:   0.003

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.071 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.002
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.077
HLM stability:   0.105
?
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):  1.741 Half-life (T1/2):  2.653

ADMET: Toxicity

hERG Blockers:  0.017 hERG Blockers (10um):  0.082
Human Hepatotoxicity (H-HT):  0.453 Drug-induced Liver Injury (DILI):  0.463
AMES Toxicity:  0.858 Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.012 Skin Sensitization:  0.995
Carcinogencity:  0.317 Eye Corrosion:  0.004
Eye Irritation:  0.715 Respiratory Toxicity:  0.013
Drug-induced Neurotoxicity:  0.026 Ototoxicity:  0.911
Hematotoxicity:  0.279 Drug-induced Nephrotoxicity:  0.496
Genotoxicity:  0.034 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.095 Hek293 Cytotoxicity:  0.071
BCF:   0.141
?
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:   1.208
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.086
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.471
?
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 NPC248743 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
0.8276 Intermediate Similarity NPC124963
0.8 Intermediate Similarity NPC326533
0.7059 Intermediate Similarity NPC233726
0.7 Intermediate Similarity NPC23134
0.6667 Remote Similarity NPC42503
0.6667 Remote Similarity NPC282143
0.6667 Remote Similarity NPC107914
0.6667 Remote Similarity NPC155457
0.6667 Remote Similarity NPC242073
0.6667 Remote Similarity NPC299781
0.6667 Remote Similarity NPC157193
0.6667 Remote Similarity NPC608193
0.6486 Remote Similarity NPC145112
0.6316 Remote Similarity NPC13143
0.6316 Remote Similarity NPC294813
0.6316 Remote Similarity NPC606861
0.6316 Remote Similarity NPC607126
0.6 Remote Similarity NPC143326
0.5833 Remote Similarity NPC31496
0.5789 Remote Similarity NPC268243
0.5714 Remote Similarity NPC317501
0.5714 Remote Similarity NPC605930
0.5682 Remote Similarity NPC206601
0.561 Remote Similarity NPC89145
0.561 Remote Similarity NPC157514
0.561 Remote Similarity NPC322314
0.561 Remote Similarity NPC269166
0.5581 Remote Similarity NPC147292
0.5476 Remote Similarity NPC100204
0.5455 Remote Similarity NPC277570
0.5455 Remote Similarity NPC63058
0.5349 Remote Similarity NPC36927
0.5349 Remote Similarity NPC262826
0.5349 Remote Similarity NPC271772
0.5319 Remote Similarity NPC71381
0.5319 Remote Similarity NPC9447
0.5319 Remote Similarity NPC263407
0.5294 Remote Similarity NPC323574
0.5227 Remote Similarity NPC150557
0.5128 Remote Similarity NPC130683
0.5122 Remote Similarity NPC603514
0.5111 Remote Similarity NPC306255
0.5106 Remote Similarity NPC12040

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC248743 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
0.7059 Intermediate Similarity NPD904 Phase 3
0.5625 Remote Similarity NPD8994 Approved
0.5556 Remote Similarity NPD905 Phase 4
0.5455 Remote Similarity NPD3181 Phase 3
0.5128 Remote Similarity NPD887 Approved
0.5128 Remote Similarity NPD895 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