Natural Product: NPC291650

Natural Product IDNPC291650
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Glucosamine
IUPAC Name (2S,3R,4R,5S,6R)-3-amino-6-(hydroxymethyl)oxane-2,4,5-triol
Synonyms Glucosamine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL606759
PubChem CID 445621
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

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 MSWZFWKMSRAUBD-UKFBFLRUSA-N
Standard InCHI InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6+/m1/s1
SMILES OC[C@H]1O[C@H](O)[C@@H]([C@H]([C@@H]1O)O)N

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   179.08 Volume:   158.724
?
Van der Waals volume.
Dense:   1.128 LogP:   -1.854
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.515
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.397
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   6.0
TPSA:   116.17
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   6.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.288 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.844 Fsp3:   1.0
MCE-18:   22.667
?
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:   0.229 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:   0.267 Promiscuous compounds:   0.062

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.347 MDCK Permeability:   -5.127
Pgp-inhibitor:   0.0 Pgp-substrate:   0.796
PAMPA:   0.988
?
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%):   0.858 30% Bioavailability (F30%):   0.992
50% Bioavailability (F50%):   0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.106 MRP1:   0.146
Plasma Protein Binding (PPB):   14.615% Volume Distribution (VD):   -0.403
Fu: 85.766%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.969
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.043
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.195 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.009
CYP2D6-inhibitor:   0.008 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.145
HLM stability:   0.025
?
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):  2.727 Half-life (T1/2):  1.895

ADMET: Toxicity

hERG Blockers:  0.009 hERG Blockers (10um):  0.129
Human Hepatotoxicity (H-HT):  0.562 Drug-induced Liver Injury (DILI):  0.546
AMES Toxicity:  0.85 Rat Oral Acute Toxicity:  0.05
Maximum Recommended Daily Dose:  0.008 Skin Sensitization:  0.996
Carcinogencity:  0.157 Eye Corrosion:  0.016
Eye Irritation:  0.824 Respiratory Toxicity:  0.03
Drug-induced Neurotoxicity:  0.03 Ototoxicity:  0.778
Hematotoxicity:  0.392 Drug-induced Nephrotoxicity:  0.765
Genotoxicity:  0.504 RPMI-8226 Immunitoxicity:  0.11
A549 Cytotoxicity:  0.092 Hek293 Cytotoxicity:  0.03
BCF:   0.109
?
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:   1.609
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.916
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.07
?
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
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11627-001-0052-8]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf980687v]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/JMPR.9000078]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. flower n.a. PMID[12130858]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18341288]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26099993]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28156114]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29400471]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[30726671]
NPO4892 Viburnum davidii Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO513 Agathosma scaberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17549 Polemonium caeruleum Species Polemoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2161 Strychnos ledermannii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1584 Tolypothrix tjipanasensis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO245 Euphorbia biglandulosa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13123 Balanophora harlandii Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29531 Lupinus cosentinii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Roots n.a. Database[FooDB]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30098 Stichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30098 Stichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30940 Bas taurus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13123 Balanophora harlandii Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29531 Lupinus cosentinii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1584 Tolypothrix tjipanasensis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17549 Polemonium caeruleum Species Polemoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4892 Viburnum davidii Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO513 Agathosma scaberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO245 Euphorbia biglandulosa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2161 Strychnos ledermannii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1637 Ganoderma japonicum Species Ganodermataceae 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 NPC291650 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 NPC322801
1.0 High Similarity NPC600826
1.0 High Similarity NPC606475
0.9615 High Similarity NPC600025
0.5161 Remote Similarity NPC73906
0.5161 Remote Similarity NPC285364
0.5161 Remote Similarity NPC255377
0.5161 Remote Similarity NPC92246
0.5161 Remote Similarity NPC165846
0.5161 Remote Similarity NPC176017
0.5161 Remote Similarity NPC21209
0.5161 Remote Similarity NPC69445
0.5161 Remote Similarity NPC289758
0.5161 Remote Similarity NPC605355

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC291650 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
1.0 High Similarity NPD9031 Approved
1.0 High Similarity NPD9032 Phase 4
1.0 High Similarity NPD9033 Approved
0.9615 High Similarity NPD9030 Approved
0.5161 Remote Similarity NPD8997 Approved
0.5161 Remote Similarity NPD8998 Phase 2
0.5161 Remote Similarity NPD8999 Phase 4
0.5161 Remote Similarity NPD9000 Phase 3

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