Natural Product: NPC252918

Natural Product IDNPC252918
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Methyl Alpha-D-Fructofuranoside
IUPAC Name (2S,3S,4S,5R)-2,5-bis(hydroxymethyl)-2-methoxyoxolane-3,4-diol
Synonyms Methyl Alpha-D-Fructofuranoside
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL450037
PubChem CID 6325664
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:0002204] C-glycosyl 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 JPHVNZOOBXUCDJ-JWXFUTCRSA-N
Standard InCHI InChI=1S/C7H14O6/c1-12-7(3-9)6(11)5(10)4(2-8)13-7/h4-6,8-11H,2-3H2,1H3/t4-,5-,6+,7+/m1/s1
SMILES OC[C@H]1O[C@@]([C@H]([C@@H]1O)O)(OC)CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   194.08 Volume:   173.813
?
Van der Waals volume.
Dense:   1.117 LogP:   -1.444
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.076
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.21
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   5.0
TPSA:   99.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.394 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.063 Fsp3:   1.0
MCE-18:   23.143
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.008 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.071
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.513 Promiscuous compounds:   0.096

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.914 MDCK Permeability:   -5.058
Pgp-inhibitor:   0.002 Pgp-substrate:   0.474
PAMPA:   0.969
?
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):   0.937
20% Bioavailability (F20%):   0.546 30% Bioavailability (F30%):   0.94
50% Bioavailability (F50%):   0.848

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.555 MRP1:   0.155
Plasma Protein Binding (PPB):   30.485% Volume Distribution (VD):   -0.337
Fu: 68.902%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.946
OATP1B3 inhibitor:   0.921 BCRP inhibitor:   0.145
BSEP inhibitor:   0.005

ADMET: Metabolism

CYP1A2-inhibitor:   0.012 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.836 CYP2C19-substrate:   0.015
CYP2C9-inhibitor:   0.396 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.373 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.093 CYP3A4-substrate:   0.058
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.041
HLM stability:   0.061
?
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):  4.285 Half-life (T1/2):  1.776

ADMET: Toxicity

hERG Blockers:  0.019 hERG Blockers (10um):  0.142
Human Hepatotoxicity (H-HT):  0.511 Drug-induced Liver Injury (DILI):  0.169
AMES Toxicity:  0.599 Rat Oral Acute Toxicity:  0.088
Maximum Recommended Daily Dose:  0.033 Skin Sensitization:  0.996
Carcinogencity:  0.291 Eye Corrosion:  0.138
Eye Irritation:  0.963 Respiratory Toxicity:  0.039
Drug-induced Neurotoxicity:  0.097 Ototoxicity:  0.691
Hematotoxicity:  0.283 Drug-induced Nephrotoxicity:  0.518
Genotoxicity:  0.022 RPMI-8226 Immunitoxicity:  0.088
A549 Cytotoxicity:  0.052 Hek293 Cytotoxicity:  0.088
BCF:   0.076
?
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:   1.368
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.367
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.718
?
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
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. leaf n.a. PMID[11348221]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[15678383]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[15844957]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[16045947]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[16378361]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits Tahiti n.a. PMID[17378609]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[17480098]
NPO8764 Laurencia decumbens Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17711344]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota roots n.a. n.a. PMID[18076142]
NPO8653 Leuconostoc mesenteroides Species Leuconostocaceae Bacteria n.a. n.a. n.a. PMID[19025748]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[19245240]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. stem n.a. PMID[20188156]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[22351977]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[24224843]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27196335]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[32083868]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[36014413]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. Malaysian n.a. PMID[7506311]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2012 Turnera diffusa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19826 Helicoverpa armigera Species Noctuidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26103 Streptomyces bobili Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO28741 Afrocarpus gracilior Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2495 Agave xylonacantha Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6766 Antiphiona pinnatisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9567 Enicosanthum cupulare Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8764 Laurencia decumbens Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8653 Leuconostoc mesenteroides Species Leuconostocaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10991 Maackia tashiroi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9136 Pseudocyclosorus subochthodes Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28741 Afrocarpus gracilior Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2012 Turnera diffusa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19826 Helicoverpa armigera Species Noctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26103 Streptomyces bobili Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6766 Antiphiona pinnatisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9567 Enicosanthum cupulare Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8653 Leuconostoc mesenteroides Species Leuconostocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10991 Maackia tashiroi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8764 Laurencia decumbens Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9136 Pseudocyclosorus subochthodes Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28741 Afrocarpus gracilior Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2495 Agave xylonacantha Species Asparagaceae 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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 30000.0 nM PMID[15844957]
NPT1 Others Radical scavenging activity n.a. IC50 > 30000.0 nM PMID[15844957]

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 NPC252918 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 NPC230789
0.5938 Remote Similarity NPC82512
0.5588 Remote Similarity NPC130683

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC252918 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
0.5588 Remote Similarity NPD887 Approved
0.5588 Remote Similarity NPD895 Phase 4

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