Natural Product: NPC311668

Natural Product IDNPC311668
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2R,3R,4R)-2-(Hydroxymethyl)Pyrrolidine-3,4-Diol
IUPAC Name (2R,3R,4R)-2-(hydroxymethyl)pyrrolidine-3,4-diol
Synonyms Imino-D-Arabinitol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL80254
PubChem CID 451991
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines

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 OQEBIHBLFRADNM-UOWFLXDJSA-N
Standard InCHI InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/p+1/t3-,4-,5-/m1/s1
SMILES C1[C@H]([C@@H]([C@@H](CO)[NH2+]1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   133.07 Volume:   123.847
?
Van der Waals volume.
Dense:   1.074 LogP:   -1.189
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.907
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.316
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   5.0
TPSA:   72.72
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   4.0 Rings:   1.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.324 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.003 Fsp3:   1.0
MCE-18:   16.8
?
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:   0.034 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.069
?
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:   0.244 Promiscuous compounds:   0.091

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.747 MDCK Permeability:   -4.848
Pgp-inhibitor:   0.005 Pgp-substrate:   0.553
PAMPA:   0.9
?
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):   0.728
20% Bioavailability (F20%):   0.526 30% Bioavailability (F30%):   0.799
50% Bioavailability (F50%):   0.81

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.317 MRP1:   0.241
Plasma Protein Binding (PPB):   17.354% Volume Distribution (VD):   -0.441
Fu: 84.68%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.795
OATP1B3 inhibitor:   0.798 BCRP inhibitor:   0.109
BSEP inhibitor:   0.011

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.012
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.424
HLM stability:   0.045
?
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):  5.561 Half-life (T1/2):  2.091

ADMET: Toxicity

hERG Blockers:  0.042 hERG Blockers (10um):  0.208
Human Hepatotoxicity (H-HT):  0.548 Drug-induced Liver Injury (DILI):  0.165
AMES Toxicity:  0.42 Rat Oral Acute Toxicity:  0.118
Maximum Recommended Daily Dose:  0.02 Skin Sensitization:  0.88
Carcinogencity:  0.142 Eye Corrosion:  0.546
Eye Irritation:  0.96 Respiratory Toxicity:  0.203
Drug-induced Neurotoxicity:  0.088 Ototoxicity:  0.798
Hematotoxicity:  0.299 Drug-induced Nephrotoxicity:  0.726
Genotoxicity:  0.022 RPMI-8226 Immunitoxicity:  0.059
A549 Cytotoxicity:  0.024 Hek293 Cytotoxicity:  0.02
BCF:   0.114
?
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:   1.374
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.388
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.641
?
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
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota pods n.a. n.a. PMID[11858756]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. PMID[15387643]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. PMID[16309326]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. root n.a. PMID[17396934]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota seeds n.a. n.a. PMID[8229017]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[9544568]
NPO7826 Agrobacterium aurantiacum Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO407 Chlorurus gibbus Species Labridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1605 Cleidion spiciflorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6450 Desmodium canum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6450 Desmodium canum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11597 Stellaria dichotoma Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6450 Desmodium canum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7826 Agrobacterium aurantiacum Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO407 Chlorurus gibbus Species Labridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1605 Cleidion spiciflorum Species Euphorbiaceae 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
NPT1667 Individual protein Liver glycogen phosphorylase Homo sapiens Ki = 400.0 nM PMID[15214781]
NPT1050 Individual protein Trehalase Rattus norvegicus IC50 = 25000.0 nM PMID[7608901]
NPT1051 Individual protein Lactase-glycosylceramidase Rattus norvegicus IC50 = 260000.0 nM PMID[7608901]
NPT1052 Individual protein Mannosidase 2 alpha 1 Rattus norvegicus IC50 = 46000.0 nM PMID[7608901]
NPT1053 Individual protein Alpha-mannosidase 2C1 Rattus norvegicus IC50 < 50000.0 nM PMID[7608901]
NPT1054 Individual protein Mannosidase 2, alpha B1 Rattus norvegicus IC50 = 110000.0 nM PMID[7608901]
NPT1052 Individual protein Mannosidase 2 alpha 1 Rattus norvegicus Ki = 35000.0 nM PMID[7608901]
NPT1053 Individual protein Alpha-mannosidase 2C1 Rattus norvegicus IC50 = 100000.0 nM PMID[2504921]
NPT1131 Individual protein Alpha-galactosidase Coffea arabica Inhibition < 50.0 % PMID[11858756]
NPT10 Individual protein Geminin Homo sapiens Potency n.a. 1258.9 nM PubChem BioAssay data set
NPT160 Individual protein TAR DNA-binding protein 43 Homo sapiens Potency n.a. 35481.3 nM PubChem BioAssay data set
NPT2681 Individual protein Glycogen phosphorylase, muscle form Oryctolagus cuniculus Ki = 400.0 nM PMID[26708111]
NPT497 Individual protein Maltase-glucoamylase Homo sapiens IC50 = 55000.0 nM PMID[7608901]
NPT462 Individual protein Sucrase-isomaltase Rattus norvegicus IC50 = 16000.0 nM PMID[11858756]
NPT462 Individual protein Sucrase-isomaltase Rattus norvegicus IC50 = 5800.0 nM PMID[11858756]
NPT462 Individual protein Sucrase-isomaltase Rattus norvegicus IC50 = 55000.0 nM PMID[18258441]
NPT509 Individual protein Beta-galactosidase Bos taurus Inhibition < 50.0 % PMID[11858756]
NPT3784 Individual protein Liver glycogen phosphorylase Rattus norvegicus IC50 = 1000.0 nM PMID[23378626]
NPT3784 Individual protein Liver glycogen phosphorylase Rattus norvegicus IC50 = 1100.0 nM PMID[23378626]
NPT462 Individual protein Sucrase-isomaltase Rattus norvegicus IC50 = 3100.0 nM PMID[35675756]
NPT497 Individual protein Maltase-glucoamylase Homo sapiens IC50 = 56000.0 nM PMID[35675756]
NPT462 Individual protein Sucrase-isomaltase Rattus norvegicus IC50 = 16000.0 nM PMID[35255314]
NPT5854 Individual protein Uncharacterized protein Sus scrofa IC50 = 2500.0 nM PMID[11858756]
NPT24816 Single protein Alpha-mannosidase Canavalia ensiformis Inhibition < 50.0 % PMID[31927314]
NPT24816 Single protein Alpha-mannosidase Canavalia ensiformis IC50 = 320000.0 nM PMID[35255314]
NPT24816 Single protein Alpha-mannosidase Canavalia ensiformis IC50 = 474000.0 nM PMID[35675756]
NPT61 Individual protein Beta-glucocerebrosidase Homo sapiens IC50 = 340000.0 nM PMID[37314161]
NPT526 Individual protein Alpha-glucosidase MAL62 Saccharomyces cerevisiae IC50 = 840.0 nM PMID[11858756]
NPT506 Individual protein Beta-mannosidase Rattus norvegicus IC50 = 290000.0 nM PMID[11858756]
NPT507 Individual protein Alpha-galactosidase Coffea arabica Inhibition < 50.0 % PMID[35255314]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Ki = 115000.0 nM PMID[36542959]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Delta Tm = 0.0 degrees C PMID[36542959]
NPT507 Individual protein Alpha-galactosidase Coffea arabica Inhibition = 4.1 % PMID[35675756]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Tm = 58.0 degrees C PMID[37314161]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Delta Tm = 4.1 degrees C PMID[36542959]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens IC50 n.a. n.a. n.a. PMID[35255314]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Delta Tm = 10.8 degrees C PMID[36542959]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Ki = 14000.0 nM PMID[37314161]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Activity = 35.0 % PMID[37314161]
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens IC50 = 56000.0 nM PMID[37314161]
NPT5874 Individual protein Glucoamylase, intracellular sporulation-specific Saccharomyces cerevisiae S288c IC50 = 150.0 nM PMID[17434740]
NPT514 Individual protein Glycogen debranching enzyme Homo sapiens IC50 = 8400.0 nM PMID[18595718]
NPT513 Individual protein Beta-glucosidase Homo sapiens IC50 = 120000.0 nM PMID[18258441]
NPT496 Individual protein Alpha-L-fucosidase 1 Bos taurus Inhibition < 50.0 % PMID[11858756]
NPT671 Individual protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 55000.0 nM PMID[11858756]
NPT671 Individual protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 55000.0 nM PMID[35255314]
NPT496 Individual protein Alpha-L-fucosidase 1 Bos taurus Inhibition = 9.0 % PMID[35675756]
NPT671 Individual protein Acidic alpha-glucosidase Rattus norvegicus IC50 = 15000.0 nM PMID[35675756]
NPT496 Individual protein Alpha-L-fucosidase 1 Bos taurus IC50 n.a. n.a. n.a. PMID[35255314]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT25 Cell line MT4 Homo sapiens EC50 > 100000.0 ug.mL-1 PMID[7608901]
NPT112 Cell line MOLT-4 Homo sapiens EC50 > 100000.0 ug.mL-1 PMID[7608901]
NPT1135 Cell line Hepatocyte Rattus norvegicus IC50 = 1000.0 nM PMID[18595718]
NPT1135 Cell line Hepatocyte Rattus norvegicus IC50 = 9000.0 nM PMID[18595718]
NPT71 Cell line HEK293 Homo sapiens Potency n.a. 5802.4 nM PubChem BioAssay data set
NPT25 Cell line MT4 Homo sapiens CC50 > 100000.0 ug.mL-1 PMID[7608901]
NPT112 Cell line MOLT-4 Homo sapiens CC50 > 100000.0 ug.mL-1 PMID[7608901]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 65.7 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 0.27 n.a. PMID[37314161]
NPT28438 Unchecked Unchecked n.a. IC50 = 87000.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 967000.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 340000.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 11000.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 4800.0 nM PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 = 2500.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 638000.0 nM PMID[35255314]
NPT28438 Unchecked Unchecked n.a. Inhibition = 5.3 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. Inhibition = 7.9 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 355000.0 nM PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 250000.0 nM PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 = 55000.0 nM PMID[35072486]
NPT28438 Unchecked Unchecked n.a. Inhibition < 50.0 % PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 = 150.0 nM PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 n.a. n.a. n.a. PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 = 362000.0 nM PMID[35255314]
NPT28438 Unchecked Unchecked n.a. IC50 = 355000.0 nM PMID[37314161]
NPT28438 Unchecked Unchecked n.a. Inhibition = 11.4 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 11000.0 nM PMID[37314161]
NPT28438 Unchecked Unchecked n.a. Inhibition = 13.5 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. Inhibition = 6.3 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. Inhibition = 13.0 % PMID[35675756]
NPT28438 Unchecked Unchecked n.a. IC50 = 1500.0 nM PMID[37314161]
NPT28438 Unchecked Unchecked n.a. IC50 = 3100.0 nM PMID[37314161]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Potency = 6513.1 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. IC50 < 50000.0 nM PMID[7608901]
NPT2 Others Unspecified n.a. IC50 = 20000.0 nM PMID[7608901]
NPT2 Others Unspecified n.a. IC50 = 130000.0 nM PMID[7608901]
NPT2 Others Unspecified n.a. Ki = 9700.0 nM PMID[7608901]
NPT2 Others Unspecified n.a. IC50 = 0.16 ug.mL-1 PMID[17378534]
NPT2 Others Unspecified n.a. IC50 = 500000.0 nM PMID[17434740]
NPT2 Others Unspecified n.a. IC50 = 200000.0 nM PMID[17434740]
NPT2 Others Unspecified n.a. IC50 = 430.0 nM PMID[18258441]
NPT2 Others Unspecified n.a. IC50 = 250000.0 nM PMID[18258441]
NPT2 Others Unspecified n.a. IC50 = 180.0 nM PMID[18258441]
NPT2 Others Unspecified n.a. IC50 = 900000.0 nM PMID[18258441]
NPT2 Others Unspecified n.a. IC50 = 110.0 nM PMID[11858756]
NPT2 Others Unspecified n.a. IC50 = 120000.0 nM PMID[11858756]
NPT2 Others Unspecified n.a. IC50 = 1200.0 nM PMID[11858756]
NPT2 Others Unspecified n.a. IC50 = 150000.0 nM PMID[11858756]
NPT2 Others Unspecified n.a. IC50 = 400000.0 nM PMID[11858756]
NPT28736 Protein family Alpha-glucosidase Saccharomyces cerevisiae S288c IC50 = 2500.0 nM PMID[37314161]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Ki = 392.0 nM PMID[23378626]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference
Macaca fascicularis n.a. Drug uptake = 62.5 % PMID[23378626]
Macaca fascicularis n.a. Drug uptake = 83.5 % PMID[23378626]
Macaca fascicularis n.a. Drug uptake = 60.8 % PMID[23378626]
Macaca fascicularis Plasma AUC = 146.0 ng.hr.mL-1 PMID[23378626]
Macaca fascicularis Plasma AUC = 40.2 ng.hr.mL-1 PMID[23378626]
Macaca fascicularis Plasma AUC = 9.66 ng.hr.mL-1 PMID[23378626]
Macaca fascicularis n.a. Tmax = 1.25 hr PMID[23378626]
Macaca fascicularis n.a. Tmax = 1.75 hr PMID[23378626]
Macaca fascicularis n.a. Tmax = 3.5 hr PMID[23378626]
Rattus norvegicus Intestine Drug uptake < 1.0 % PMID[23378626]
Rattus norvegicus Stomach Drug uptake < 1.0 % PMID[23378626]





 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 NPC311668 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
0.5789 Remote Similarity NPC8087

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC311668 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