Natural Product: NPC125972

Natural Product IDNPC125972
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YTILFWGKUNLJMX-YMILTQATSA-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: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 YTILFWGKUNLJMX-YMILTQATSA-N
Standard InCHI InChI=1S/C16H22O9/c1-7(18)12-9(23-3)4-8(22-2)5-10(12)24-16-15(21)14(20)13(19)11(6-17)25-16/h4-5,11,13-17,19-21H,6H2,1-3H3/t11-,13-,14+,15-,16-/m1/s1
SMILES CC(=O)c1c(cc(cc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   358.13 Volume:   336.746
?
Van der Waals volume.
Dense:   1.064 LogP:   -0.311
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.03
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.147
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   13.0
TPSA:   134.91
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.476 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.581 Fsp3:   0.562
MCE-18:   54.4
?
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:   0.455 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.06
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.044
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.201 Promiscuous compounds:   0.205

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.617 MDCK Permeability:   -4.975
Pgp-inhibitor:   0.001 Pgp-substrate:   0.076
PAMPA:   0.744
?
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):   0.327
20% Bioavailability (F20%):   0.014 30% Bioavailability (F30%):   0.342
50% Bioavailability (F50%):   0.625

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.081 MRP1:   0.395
Plasma Protein Binding (PPB):   63.674% Volume Distribution (VD):   -0.14
Fu: 36.528%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.176
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.042 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.041 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.007
HLM stability:   0.007
?
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):  2.663 Half-life (T1/2):  3.089

ADMET: Toxicity

hERG Blockers:  0.036 hERG Blockers (10um):  0.139
Human Hepatotoxicity (H-HT):  0.704 Drug-induced Liver Injury (DILI):  0.848
AMES Toxicity:  0.893 Rat Oral Acute Toxicity:  0.031
Maximum Recommended Daily Dose:  0.025 Skin Sensitization:  0.978
Carcinogencity:  0.392 Eye Corrosion:  0.0
Eye Irritation:  0.368 Respiratory Toxicity:  0.037
Drug-induced Neurotoxicity:  0.076 Ototoxicity:  0.898
Hematotoxicity:  0.57 Drug-induced Nephrotoxicity:  0.685
Genotoxicity:  0.276 RPMI-8226 Immunitoxicity:  0.118
A549 Cytotoxicity:  0.183 Hek293 Cytotoxicity:  0.154
BCF:   0.299
?
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:   2.706
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.159
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.366
?
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
NPO13784 Dalbergia candenatensis Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[19653666]
NPO12711 Ligularia altaica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20073490]
NPO4576 Corynandra viscosa Species Cleomaceae Eukaryota n.a. leaf n.a. PMID[28135851]
NPO13784 Dalbergia candenatensis Species Fabaceae Eukaryota n.a. Thai n.a. PMID[3430167]
NPO15113 Poterioochromonas malhamensis Species Ochromonadaceae Eukaryota n.a. n.a. n.a. PMID[8021653]
NPO25680 Ramalina siliquosa Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12711 Ligularia altaica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9612 Dryopteris dilatata Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13784 Dalbergia candenatensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4576 Corynandra viscosa Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10319 Calycodendron milnei n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO15113 Poterioochromonas malhamensis Species Ochromonadaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4576 Corynandra viscosa Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15113 Poterioochromonas malhamensis Species Ochromonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25680 Ramalina siliquosa Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4576 Corynandra viscosa Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9612 Dryopteris dilatata Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13784 Dalbergia candenatensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10319 Calycodendron milnei n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12711 Ligularia altaica Species Asteraceae 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 NPC125972 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
0.7647 Intermediate Similarity NPC218685
0.717 Intermediate Similarity NPC23084
0.6735 Remote Similarity NPC217854
0.66 Remote Similarity NPC294470
0.6531 Remote Similarity NPC276195
0.6275 Remote Similarity NPC153149
0.6154 Remote Similarity NPC25817
0.6061 Remote Similarity NPC206378
0.6038 Remote Similarity NPC299144
0.5962 Remote Similarity NPC192810
0.5882 Remote Similarity NPC212729
0.5882 Remote Similarity NPC604498
0.5849 Remote Similarity NPC152722
0.5818 Remote Similarity NPC221090
0.5818 Remote Similarity NPC69513
0.5806 Remote Similarity NPC479030
0.5781 Remote Similarity NPC178851
0.5781 Remote Similarity NPC99233
0.5769 Remote Similarity NPC269242
0.5741 Remote Similarity NPC60589
0.5741 Remote Similarity NPC469708
0.5741 Remote Similarity NPC609376
0.5714 Remote Similarity NPC48863
0.5714 Remote Similarity NPC214454
0.5714 Remote Similarity NPC251981
0.5714 Remote Similarity NPC13745
0.5714 Remote Similarity NPC228907
0.5714 Remote Similarity NPC604892
0.569 Remote Similarity NPC479028
0.569 Remote Similarity NPC479031
0.5636 Remote Similarity NPC200092
0.5636 Remote Similarity NPC226712
0.5636 Remote Similarity NPC608788
0.5614 Remote Similarity NPC215833
0.5593 Remote Similarity NPC210478
0.5577 Remote Similarity NPC142319
0.5571 Remote Similarity NPC473202
0.5536 Remote Similarity NPC80098
0.5536 Remote Similarity NPC145900
0.5522 Remote Similarity NPC76128
0.5517 Remote Similarity NPC49074
0.5469 Remote Similarity NPC474044
0.5469 Remote Similarity NPC216752
0.5455 Remote Similarity NPC606849
0.5439 Remote Similarity NPC166040
0.5439 Remote Similarity NPC95292
0.5424 Remote Similarity NPC162093
0.5424 Remote Similarity NPC270849
0.5424 Remote Similarity NPC205054
0.5424 Remote Similarity NPC606892
0.541 Remote Similarity NPC106025
0.5362 Remote Similarity NPC106625
0.5345 Remote Similarity NPC40377
0.5333 Remote Similarity NPC26653
0.5323 Remote Similarity NPC232673
0.5323 Remote Similarity NPC97326
0.5246 Remote Similarity NPC479029
0.5238 Remote Similarity NPC199335
0.5238 Remote Similarity NPC477240
0.5224 Remote Similarity NPC30432
0.5224 Remote Similarity NPC605700
0.5217 Remote Similarity NPC61594
0.5217 Remote Similarity NPC219163
0.5211 Remote Similarity NPC300537
0.5179 Remote Similarity NPC604439
0.5167 Remote Similarity NPC472024
0.5167 Remote Similarity NPC604356
0.5161 Remote Similarity NPC95392
0.5161 Remote Similarity NPC84013
0.5161 Remote Similarity NPC55715
0.5161 Remote Similarity NPC35877
0.5161 Remote Similarity NPC104167
0.5156 Remote Similarity NPC190217
0.5156 Remote Similarity NPC611586
0.5152 Remote Similarity NPC210192
0.5147 Remote Similarity NPC108674
0.5147 Remote Similarity NPC604833
0.5143 Remote Similarity NPC56735
0.5143 Remote Similarity NPC147596
0.5088 Remote Similarity NPC12308
0.5085 Remote Similarity NPC310661
0.5085 Remote Similarity NPC9912
0.5082 Remote Similarity NPC80600
0.5082 Remote Similarity NPC164599
0.5079 Remote Similarity NPC473045
0.5079 Remote Similarity NPC247146
0.5079 Remote Similarity NPC34456
0.5075 Remote Similarity NPC177742
0.5072 Remote Similarity NPC308265

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC125972 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