Natural Product: NPC216429

Natural Product IDNPC216429
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SFLMUHDGSQZDOW-IBEHDNSVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 73171
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 SFLMUHDGSQZDOW-IBEHDNSVSA-N
Standard InCHI InChI=1S/C16H22O8/c1-22-11-7-9(3-2-6-17)4-5-10(11)23-16-15(21)14(20)13(19)12(8-18)24-16/h2-5,7,12-21H,6,8H2,1H3/t12-,13-,14+,15-,16-/m1/s1
SMILES COc1cc(C=CCO)ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   342.13 Volume:   327.955
?
Van der Waals volume.
Dense:   1.043 LogP:   -0.186
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.46
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.583
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   13.0
TPSA:   128.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   5.0 Rings:   2.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.44 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.63 Fsp3:   0.5
MCE-18:   47.833
?
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:   0.431 Fluc inhibitor:   0.477
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.139
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.102
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.254 Promiscuous compounds:   0.219

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.926 MDCK Permeability:   -5.034
Pgp-inhibitor:   0.0 Pgp-substrate:   0.205
PAMPA:   0.96
?
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):   0.912
20% Bioavailability (F20%):   0.371 30% Bioavailability (F30%):   0.974
50% Bioavailability (F50%):   0.951

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.066 MRP1:   0.039
Plasma Protein Binding (PPB):   60.182% Volume Distribution (VD):   -0.461
Fu: 42.305%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.263
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.099
HLM stability:   0.06
?
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):  2.842 Half-life (T1/2):  3.14

ADMET: Toxicity

hERG Blockers:  0.04 hERG Blockers (10um):  0.111
Human Hepatotoxicity (H-HT):  0.725 Drug-induced Liver Injury (DILI):  0.467
AMES Toxicity:  0.929 Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.012 Skin Sensitization:  0.999
Carcinogencity:  0.279 Eye Corrosion:  0.001
Eye Irritation:  0.649 Respiratory Toxicity:  0.027
Drug-induced Neurotoxicity:  0.093 Ototoxicity:  0.962
Hematotoxicity:  0.215 Drug-induced Nephrotoxicity:  0.743
Genotoxicity:  0.044 RPMI-8226 Immunitoxicity:  0.091
A549 Cytotoxicity:  0.236 Hek293 Cytotoxicity:  0.065
BCF:   0.274
?
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:   2.556
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.22
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.241
?
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
NPO5547 Hypericum prolificum Species Hypericaceae Eukaryota aerial parts n.a. n.a. PMID[17125240]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota stem bark Kunming, Yunnan Province, China n.a. PMID[18986199]
NPO10230 Trichilia connaroides Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[31589431]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21329 Ilyonectria destructans Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23754 Solanum aculeatissimum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10211 Pajanelia multijuga n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10230 Trichilia connaroides Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12339 Daphne feddei Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5547 Hypericum prolificum Species Hypericaceae 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 NPC216429 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 NPC248355
0.8333 Intermediate Similarity NPC55040
0.8182 Intermediate Similarity NPC302378
0.7593 Intermediate Similarity NPC49074
0.7167 Intermediate Similarity NPC37468
0.6909 Remote Similarity NPC166040
0.6897 Remote Similarity NPC479029
0.6885 Remote Similarity NPC604095
0.6842 Remote Similarity NPC270849
0.6812 Remote Similarity NPC43508
0.6667 Remote Similarity NPC93924
0.6552 Remote Similarity NPC472024
0.65 Remote Similarity NPC104167
0.6441 Remote Similarity NPC26653
0.6441 Remote Similarity NPC80600
0.6441 Remote Similarity NPC210478
0.6271 Remote Similarity NPC162093
0.6271 Remote Similarity NPC479028
0.6271 Remote Similarity NPC479031
0.625 Remote Similarity NPC200092
0.6207 Remote Similarity NPC9912
0.6078 Remote Similarity NPC228907
0.6027 Remote Similarity NPC157816
0.6 Remote Similarity NPC164857
0.6 Remote Similarity NPC604356
0.5938 Remote Similarity NPC276753
0.5938 Remote Similarity NPC205796
0.5921 Remote Similarity NPC478985
0.5893 Remote Similarity NPC25817
0.5846 Remote Similarity NPC246947
0.58 Remote Similarity NPC227894
0.5781 Remote Similarity NPC470236
0.5692 Remote Similarity NPC294166
0.5692 Remote Similarity NPC115022
0.5672 Remote Similarity NPC475084
0.5647 Remote Similarity NPC488385
0.5645 Remote Similarity NPC481303
0.5625 Remote Similarity NPC232673
0.5606 Remote Similarity NPC479030
0.5571 Remote Similarity NPC158635
0.5571 Remote Similarity NPC229882
0.5556 Remote Similarity NPC469654
0.5538 Remote Similarity NPC100389
0.5517 Remote Similarity NPC299144
0.5493 Remote Similarity NPC286235
0.5488 Remote Similarity NPC223335
0.5488 Remote Similarity NPC40920
0.5484 Remote Similarity NPC251102
0.5484 Remote Similarity NPC210298
0.5443 Remote Similarity NPC269559
0.5439 Remote Similarity NPC153149
0.5422 Remote Similarity NPC44507
0.5417 Remote Similarity NPC38041
0.5417 Remote Similarity NPC18979
0.5417 Remote Similarity NPC22150
0.5357 Remote Similarity NPC276195
0.5357 Remote Similarity NPC212729
0.5357 Remote Similarity NPC604498
0.5342 Remote Similarity NPC471063
0.5333 Remote Similarity NPC69513
0.5263 Remote Similarity NPC217854
0.5263 Remote Similarity NPC269242
0.5254 Remote Similarity NPC60589
0.5254 Remote Similarity NPC469708
0.5254 Remote Similarity NPC609376
0.5246 Remote Similarity NPC48863
0.5246 Remote Similarity NPC251981
0.5246 Remote Similarity NPC13745
0.5217 Remote Similarity NPC98777
0.5205 Remote Similarity NPC227902
0.5205 Remote Similarity NPC279298
0.5195 Remote Similarity NPC470413
0.5195 Remote Similarity NPC39657
0.5172 Remote Similarity NPC192810
0.5172 Remote Similarity NPC294470
0.5167 Remote Similarity NPC226712
0.5167 Remote Similarity NPC608788
0.5161 Remote Similarity NPC215833
0.5156 Remote Similarity NPC26080
0.5156 Remote Similarity NPC165686
0.5147 Remote Similarity NPC202700
0.5147 Remote Similarity NPC185778
0.5143 Remote Similarity NPC295970
0.5085 Remote Similarity NPC55300
0.5085 Remote Similarity NPC152722
0.5082 Remote Similarity NPC145900
0.5079 Remote Similarity NPC218685
0.5075 Remote Similarity NPC157554
0.5068 Remote Similarity NPC488085
0.5067 Remote Similarity NPC469559
0.5063 Remote Similarity NPC470950

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC216429 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
0.5167 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