Natural Product: NPC136955

Natural Product IDNPC136955
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YAQRKKHRLWWZGG-IBEHDNSVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11972388
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 YAQRKKHRLWWZGG-IBEHDNSVSA-N
Standard InCHI InChI=1S/C16H24O9/c1-23-11-4-8(9(5-17)6-18)2-3-10(11)24-16-15(22)14(21)13(20)12(7-19)25-16/h2-4,9,12-22H,5-7H2,1H3/t12-,13-,14+,15-,16-/m1/s1
SMILES COc1cc(ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(CO)CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   360.14 Volume:   339.382
?
Van der Waals volume.
Dense:   1.061 LogP:   -0.901
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.352
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.139
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   12.0
TPSA:   149.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   6.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.323 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.706 Fsp3:   0.625
MCE-18:   50.769
?
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:   0.381 Fluc inhibitor:   0.018
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.045
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.082
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.235 Promiscuous compounds:   0.042

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.386 MDCK Permeability:   -4.864
Pgp-inhibitor:   0.0 Pgp-substrate:   0.303
PAMPA:   0.952
?
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):   0.93
20% Bioavailability (F20%):   0.075 30% Bioavailability (F30%):   0.709
50% Bioavailability (F50%):   0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.106 MRP1:   0.059
Plasma Protein Binding (PPB):   38.87% Volume Distribution (VD):   -0.389
Fu: 62.961%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.986
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.465
BSEP inhibitor:   0.025

ADMET: Metabolism

CYP1A2-inhibitor:   0.018 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
HLM stability:   0.039
?
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):  2.199 Half-life (T1/2):  3.197

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.035
Human Hepatotoxicity (H-HT):  0.79 Drug-induced Liver Injury (DILI):  0.551
AMES Toxicity:  0.778 Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.006 Skin Sensitization:  0.992
Carcinogencity:  0.282 Eye Corrosion:  0.0
Eye Irritation:  0.082 Respiratory Toxicity:  0.002
Drug-induced Neurotoxicity:  0.009 Ototoxicity:  0.992
Hematotoxicity:  0.396 Drug-induced Nephrotoxicity:  0.775
Genotoxicity:  0.024 RPMI-8226 Immunitoxicity:  0.074
A549 Cytotoxicity:  0.133 Hek293 Cytotoxicity:  0.07
BCF:   0.197
?
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:   2.215
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.752
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.844
?
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
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. seed n.a. DOI[10.1016/j.indcrop.2012.04.060]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(02)00288-1]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36432786]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4384 Cetraria aculeata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12620 Carum carvi Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO12620 Carum carvi Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO12620 Carum carvi Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4384 Cetraria aculeata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12620 Carum carvi 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 NPC136955 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
0.76 Intermediate Similarity NPC166040
0.717 Intermediate Similarity NPC472024
0.717 Intermediate Similarity NPC270849
0.7037 Intermediate Similarity NPC26653
0.7037 Intermediate Similarity NPC80600
0.6909 Remote Similarity NPC248355
0.6786 Remote Similarity NPC55040
0.6739 Remote Similarity NPC228907
0.6667 Remote Similarity NPC302378
0.6481 Remote Similarity NPC9912
0.6471 Remote Similarity NPC25817
0.6441 Remote Similarity NPC276753
0.6441 Remote Similarity NPC205796
0.6333 Remote Similarity NPC37468
0.6333 Remote Similarity NPC246947
0.6333 Remote Similarity NPC604095
0.6316 Remote Similarity NPC479029
0.6038 Remote Similarity NPC299144
0.5965 Remote Similarity NPC479028
0.5965 Remote Similarity NPC479031
0.5962 Remote Similarity NPC153149
0.5882 Remote Similarity NPC276195
0.5882 Remote Similarity NPC212729
0.5882 Remote Similarity NPC604498
0.5821 Remote Similarity NPC279298
0.5818 Remote Similarity NPC69513
0.5769 Remote Similarity NPC217854
0.5769 Remote Similarity NPC269242
0.5758 Remote Similarity NPC158635
0.5758 Remote Similarity NPC229882
0.5741 Remote Similarity NPC609376
0.5714 Remote Similarity NPC48863
0.5714 Remote Similarity NPC251981
0.5714 Remote Similarity NPC13745
0.5672 Remote Similarity NPC286235
0.566 Remote Similarity NPC294470
0.5636 Remote Similarity NPC226712
0.5636 Remote Similarity NPC608788
0.5614 Remote Similarity NPC215833
0.5593 Remote Similarity NPC210478
0.5588 Remote Similarity NPC38041
0.5588 Remote Similarity NPC227902
0.5588 Remote Similarity NPC18979
0.5588 Remote Similarity NPC22150
0.5556 Remote Similarity NPC152722
0.5536 Remote Similarity NPC145900
0.5517 Remote Similarity NPC218685
0.5517 Remote Similarity NPC49074
0.5507 Remote Similarity NPC471063
0.5493 Remote Similarity NPC217635
0.5455 Remote Similarity NPC60589
0.5455 Remote Similarity NPC469708
0.5424 Remote Similarity NPC162093
0.5417 Remote Similarity NPC43508
0.541 Remote Similarity NPC104167
0.5397 Remote Similarity NPC294166
0.5397 Remote Similarity NPC115022
0.5373 Remote Similarity NPC212290
0.537 Remote Similarity NPC192810
0.5357 Remote Similarity NPC200092
0.5323 Remote Similarity NPC247146
0.5312 Remote Similarity NPC479030
0.5283 Remote Similarity NPC142319
0.5278 Remote Similarity NPC93924
0.5263 Remote Similarity NPC221090
0.5263 Remote Similarity NPC80098
0.5231 Remote Similarity NPC146803
0.5224 Remote Similarity NPC148273
0.5217 Remote Similarity NPC61594
0.5172 Remote Similarity NPC95292
0.5167 Remote Similarity NPC205054
0.5167 Remote Similarity NPC23084
0.5167 Remote Similarity NPC604356
0.5161 Remote Similarity NPC95392
0.5161 Remote Similarity NPC84013
0.5161 Remote Similarity NPC222455
0.5161 Remote Similarity NPC55715
0.5161 Remote Similarity NPC35877
0.5152 Remote Similarity NPC210192
0.5152 Remote Similarity NPC175275
0.5152 Remote Similarity NPC475096
0.5152 Remote Similarity NPC475084
0.5143 Remote Similarity NPC56735
0.5135 Remote Similarity NPC299706
0.5135 Remote Similarity NPC245615
0.5135 Remote Similarity NPC186316
0.5135 Remote Similarity NPC115466
0.5135 Remote Similarity NPC39657
0.5135 Remote Similarity NPC61604
0.5088 Remote Similarity NPC12308
0.5085 Remote Similarity NPC310661
0.5079 Remote Similarity NPC232673
0.5077 Remote Similarity NPC486107

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC136955 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
0.5636 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