Natural Product: NPC82948

Natural Product IDNPC82948
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 URINFYYBTXOQCT-OUUBHVDSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11972303
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 URINFYYBTXOQCT-OUUBHVDSSA-N
Standard InCHI InChI=1S/C20H24O8/c21-9-16-17(23)18(24)19(25)20(28-16)27-15-7-3-13(4-8-15)11-26-10-12-1-5-14(22)6-2-12/h1-8,16-25H,9-11H2/t16-,17-,18+,19-,20-/m1/s1
SMILES c1cc(ccc1COCc1ccc(cc1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   392.15 Volume:   383.31
?
Van der Waals volume.
Dense:   1.023 LogP:   0.176
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.562
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.323
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   18.0
TPSA:   128.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.455 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.393 Fsp3:   0.4
MCE-18:   60.429
?
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:   0.6 Fluc inhibitor:   0.194
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.132
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.197
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.167 Promiscuous compounds:   0.247

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.535 MDCK Permeability:   -4.939
Pgp-inhibitor:   0.002 Pgp-substrate:   0.002
PAMPA:   0.844
?
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):   0.963
20% Bioavailability (F20%):   0.119 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.253

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.085 MRP1:   0.045
Plasma Protein Binding (PPB):   86.237% Volume Distribution (VD):   0.101
Fu: 12.988%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.262
BSEP inhibitor:   0.35

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.008
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.943 CYP3A4-substrate:   0.368
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.759
HLM stability:   0.31
?
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):  2.947 Half-life (T1/2):  2.006

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.4
Human Hepatotoxicity (H-HT):  0.23 Drug-induced Liver Injury (DILI):  0.397
AMES Toxicity:  0.653 Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.016 Skin Sensitization:  0.958
Carcinogencity:  0.05 Eye Corrosion:  0.0
Eye Irritation:  0.719 Respiratory Toxicity:  0.07
Drug-induced Neurotoxicity:  0.008 Ototoxicity:  0.497
Hematotoxicity:  0.053 Drug-induced Nephrotoxicity:  0.469
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.028
A549 Cytotoxicity:  0.128 Hek293 Cytotoxicity:  0.118
BCF:   1.069
?
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:   3.552
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.142
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.358
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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
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. tuber n.a. PMID[15180301]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[17381154]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[25843525]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22309 Gastrodia elata Species Orchidaceae 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 NPC82948 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
0.7 Intermediate Similarity NPC142319
0.6818 Remote Similarity NPC160882
0.6346 Remote Similarity NPC212729
0.6346 Remote Similarity NPC604498
0.6271 Remote Similarity NPC214910
0.6226 Remote Similarity NPC269242
0.6212 Remote Similarity NPC186406
0.6111 Remote Similarity NPC175771
0.6111 Remote Similarity NPC294470
0.6053 Remote Similarity NPC605959
0.6053 Remote Similarity NPC606999
0.6 Remote Similarity NPC248119
0.6 Remote Similarity NPC26080
0.6 Remote Similarity NPC165686
0.5974 Remote Similarity NPC600084
0.5968 Remote Similarity NPC85799
0.5968 Remote Similarity NPC303422
0.5909 Remote Similarity NPC264381
0.5893 Remote Similarity NPC60589
0.5893 Remote Similarity NPC469708
0.5893 Remote Similarity NPC609376
0.5846 Remote Similarity NPC121001
0.5821 Remote Similarity NPC471029
0.5821 Remote Similarity NPC601944
0.5789 Remote Similarity NPC200092
0.575 Remote Similarity NPC606350
0.5714 Remote Similarity NPC9248
0.5714 Remote Similarity NPC169968
0.569 Remote Similarity NPC80098
0.5672 Remote Similarity NPC259767
0.5672 Remote Similarity NPC57587
0.5652 Remote Similarity NPC170475
0.5634 Remote Similarity NPC97240
0.5593 Remote Similarity NPC166168
0.5571 Remote Similarity NPC169761
0.5538 Remote Similarity NPC294166
0.5538 Remote Similarity NPC115022
0.5522 Remote Similarity NPC302989
0.5517 Remote Similarity NPC12308
0.5507 Remote Similarity NPC271479
0.55 Remote Similarity NPC40377
0.5455 Remote Similarity NPC8497
0.5441 Remote Similarity NPC99233
0.5429 Remote Similarity NPC191046
0.5424 Remote Similarity NPC221090
0.5397 Remote Similarity NPC57751
0.5385 Remote Similarity NPC478871
0.5385 Remote Similarity NPC478870
0.5385 Remote Similarity NPC478872
0.5385 Remote Similarity NPC478873
0.5362 Remote Similarity NPC92054
0.5362 Remote Similarity NPC165720
0.5362 Remote Similarity NPC148273
0.5357 Remote Similarity NPC484157
0.5352 Remote Similarity NPC39351
0.5345 Remote Similarity NPC604439
0.5333 Remote Similarity NPC214454
0.5323 Remote Similarity NPC251102
0.5323 Remote Similarity NPC479028
0.5323 Remote Similarity NPC205054
0.5323 Remote Similarity NPC210298
0.5323 Remote Similarity NPC479031
0.5323 Remote Similarity NPC604356
0.5303 Remote Similarity NPC242028
0.5303 Remote Similarity NPC203230
0.5303 Remote Similarity NPC252169
0.5294 Remote Similarity NPC212770
0.5294 Remote Similarity NPC603951
0.5294 Remote Similarity NPC606158
0.5286 Remote Similarity NPC169248
0.5286 Remote Similarity NPC72649
0.5283 Remote Similarity NPC228907
0.5278 Remote Similarity NPC206378
0.5278 Remote Similarity NPC106625
0.527 Remote Similarity NPC68265
0.5263 Remote Similarity NPC153149
0.5263 Remote Similarity NPC192810
0.5246 Remote Similarity NPC310661
0.5231 Remote Similarity NPC218003
0.5217 Remote Similarity NPC177742
0.5211 Remote Similarity NPC308265
0.5211 Remote Similarity NPC259182
0.5211 Remote Similarity NPC185103
0.5205 Remote Similarity NPC145319
0.5205 Remote Similarity NPC166180
0.5179 Remote Similarity NPC276195
0.5172 Remote Similarity NPC25817
0.5172 Remote Similarity NPC152722
0.5167 Remote Similarity NPC145900
0.5161 Remote Similarity NPC218685
0.5147 Remote Similarity NPC260681
0.5143 Remote Similarity NPC601828
0.5139 Remote Similarity NPC471457
0.5139 Remote Similarity NPC26195
0.5088 Remote Similarity NPC217854
0.5079 Remote Similarity NPC83975
0.5079 Remote Similarity NPC23084
0.5079 Remote Similarity NPC19470
0.5077 Remote Similarity NPC222455
0.5075 Remote Similarity NPC65530
0.5072 Remote Similarity NPC98777
0.5068 Remote Similarity NPC472353
0.5065 Remote Similarity NPC600240
0.5065 Remote Similarity NPC609745

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC82948 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
NPD

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