Natural Product: NPC498929

Natural Product IDNPC498929
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 4-Hydroxystyrene 4-O-alpha-D-galactopyranoside
IUPAC Name (2~{R},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-(4-vinylphenoxy)tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic 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 UBOROQNWLSDLJF-XHJNMGKDSA-N
Standard InCHI InChI=1S/C14H18O6/c1-2-8-3-5-9(6-4-8)19-14-13(18)12(17)11(16)10(7-15)20-14/h2-6,10-18H,1,7H2/t10-,11+,12-,13+,14-/m1/s1
SMILES C=CC1=CC=C(O[C@@H]2O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)C=C1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   282.11 Volume:   275.783
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Van der Waals volume.
Dense:   1.023 LogP:   0.355
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.718
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.305
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   13.0
TPSA:   99.38
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Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.594 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.477 Fsp3:   0.429
MCE-18:   45.5
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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:   0.489 Fluc inhibitor:   0.126
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.032
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.035
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.433 Promiscuous compounds:   0.066

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.58 MDCK Permeability:   -4.898
Pgp-inhibitor:   0.001 Pgp-substrate:   0.032
PAMPA:   0.981
?
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):   0.993
20% Bioavailability (F20%):   0.995 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.002
Plasma Protein Binding (PPB):   78.703% Volume Distribution (VD):   -0.218
Fu: 22.11%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.99
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.335
BSEP inhibitor:   0.042

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.238 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.881
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.975
HLM stability:   0.049
?
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):  3.165 Half-life (T1/2):  1.993

ADMET: Toxicity

hERG Blockers:  0.023 hERG Blockers (10um):  0.154
Human Hepatotoxicity (H-HT):  0.661 Drug-induced Liver Injury (DILI):  0.761
AMES Toxicity:  0.97 Rat Oral Acute Toxicity:  0.102
Maximum Recommended Daily Dose:  0.016 Skin Sensitization:  1.0
Carcinogencity:  0.355 Eye Corrosion:  0.01
Eye Irritation:  0.83 Respiratory Toxicity:  0.092
Drug-induced Neurotoxicity:  0.247 Ototoxicity:  0.79
Hematotoxicity:  0.65 Drug-induced Nephrotoxicity:  0.808
Genotoxicity:  0.113 RPMI-8226 Immunitoxicity:  0.129
A549 Cytotoxicity:  0.712 Hek293 Cytotoxicity:  0.194
BCF:   0.529
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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:   2.928
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.356
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.537
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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
NPO40635 Streptomyces sp. Q22 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[28504888]
NPO40635 Streptomyces sp. Q22 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]

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 NPC498929 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
0.8182 Intermediate Similarity NPC200092
0.7857 Intermediate Similarity NPC212729
0.7857 Intermediate Similarity NPC604498
0.7674 Intermediate Similarity NPC269242
0.7556 Intermediate Similarity NPC60589
0.7556 Intermediate Similarity NPC469708
0.75 Intermediate Similarity NPC294470
0.7347 Intermediate Similarity NPC251102
0.7347 Intermediate Similarity NPC210298
0.7347 Intermediate Similarity NPC604356
0.72 Intermediate Similarity NPC26080
0.72 Intermediate Similarity NPC165686
0.7174 Intermediate Similarity NPC609376
0.7 Intermediate Similarity NPC479028
0.7 Intermediate Similarity NPC479031
0.6875 Remote Similarity NPC80098
0.6667 Remote Similarity NPC142319
0.6512 Remote Similarity NPC228907
0.625 Remote Similarity NPC294166
0.625 Remote Similarity NPC115022
0.6226 Remote Similarity NPC481303
0.6154 Remote Similarity NPC218685
0.6122 Remote Similarity NPC604439
0.6111 Remote Similarity NPC248355
0.6111 Remote Similarity NPC479029
0.6102 Remote Similarity NPC259767
0.6102 Remote Similarity NPC295970
0.6042 Remote Similarity NPC153149
0.6 Remote Similarity NPC55040
0.6 Remote Similarity NPC226712
0.6 Remote Similarity NPC608788
0.5962 Remote Similarity NPC9912
0.5957 Remote Similarity NPC276195
0.5926 Remote Similarity NPC214910
0.5918 Remote Similarity NPC25817
0.5893 Remote Similarity NPC302378
0.5893 Remote Similarity NPC59324
0.5862 Remote Similarity NPC479030
0.5862 Remote Similarity NPC37468
0.5862 Remote Similarity NPC186418
0.5862 Remote Similarity NPC8497
0.5833 Remote Similarity NPC217854
0.5806 Remote Similarity NPC185103
0.5789 Remote Similarity NPC100389
0.5769 Remote Similarity NPC214454
0.5769 Remote Similarity NPC166040
0.5741 Remote Similarity NPC270849
0.5741 Remote Similarity NPC19470
0.5714 Remote Similarity NPC192810
0.5686 Remote Similarity NPC12308
0.5667 Remote Similarity NPC248119
0.5667 Remote Similarity NPC98777
0.566 Remote Similarity NPC310661
0.5645 Remote Similarity NPC186406
0.5636 Remote Similarity NPC210478
0.5614 Remote Similarity NPC85799
0.5614 Remote Similarity NPC303422
0.5614 Remote Similarity NPC218003
0.56 Remote Similarity NPC9248
0.5593 Remote Similarity NPC202700
0.5593 Remote Similarity NPC604095
0.5577 Remote Similarity NPC221090
0.5574 Remote Similarity NPC57587
0.5556 Remote Similarity NPC49074
0.5517 Remote Similarity NPC146540
0.551 Remote Similarity NPC484157
0.549 Remote Similarity NPC299144
0.5484 Remote Similarity NPC606353
0.5472 Remote Similarity NPC166168
0.5469 Remote Similarity NPC488085
0.5455 Remote Similarity NPC472024
0.5455 Remote Similarity NPC162093
0.5455 Remote Similarity NPC205054
0.5455 Remote Similarity NPC23084
0.5455 Remote Similarity NPC606892
0.5439 Remote Similarity NPC222455
0.5424 Remote Similarity NPC242028
0.5424 Remote Similarity NPC203230
0.541 Remote Similarity NPC175275
0.537 Remote Similarity NPC40377
0.5357 Remote Similarity NPC26653
0.5357 Remote Similarity NPC210015
0.5357 Remote Similarity NPC80600
0.5357 Remote Similarity NPC164599
0.5345 Remote Similarity NPC232673
0.5333 Remote Similarity NPC185778
0.5323 Remote Similarity NPC264381
0.5294 Remote Similarity NPC152722
0.5283 Remote Similarity NPC69513
0.5283 Remote Similarity NPC145900
0.5246 Remote Similarity NPC474044
0.5238 Remote Similarity NPC471029
0.5238 Remote Similarity NPC601944
0.5238 Remote Similarity NPC605700
0.5224 Remote Similarity NPC607190
0.5192 Remote Similarity NPC198798
0.5185 Remote Similarity NPC48863
0.5185 Remote Similarity NPC251981
0.5185 Remote Similarity NPC13745
0.5179 Remote Similarity NPC485268
0.5179 Remote Similarity NPC83975
0.5172 Remote Similarity NPC104167
0.5167 Remote Similarity NPC252169
0.5167 Remote Similarity NPC65530
0.5161 Remote Similarity NPC210192
0.5161 Remote Similarity NPC212770
0.5161 Remote Similarity NPC475084
0.5152 Remote Similarity NPC48640
0.5094 Remote Similarity NPC36434
0.5091 Remote Similarity NPC215833
0.5085 Remote Similarity NPC34456
0.5082 Remote Similarity NPC479374
0.5082 Remote Similarity NPC610808
0.5077 Remote Similarity NPC170475
0.5072 Remote Similarity NPC93924

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC498929 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
0.6 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