Structure

Physi-Chem Properties

Molecular Weight:  265.11
Volume:  258.418
LogP:  -1.681
LogD:  -0.044
LogS:  -1.172
# Rotatable Bonds:  4
TPSA:  76.64
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.702
Synthetic Accessibility Score:  3.797
Fsp3:  0.417
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.172
MDCK Permeability:  1.8201733837486245e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.409
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.831
Plasma Protein Binding (PPB):  27.40276336669922%
Volume Distribution (VD):  1.082
Pgp-substrate:  65.99797058105469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.072
CYP1A2-substrate:  0.218
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.044
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.043
CYP2D6-inhibitor:  0.184
CYP2D6-substrate:  0.401
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.168

ADMET: Excretion

Clearance (CL):  6.681
Half-life (T1/2):  0.904

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.904
Drug-inuced Liver Injury (DILI):  0.109
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.881
Skin Sensitization:  0.25
Carcinogencity:  0.772
Eye Corrosion:  0.003
Eye Irritation:  0.039
Respiratory Toxicity:  0.684

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  Natural Product: NPC125076

Natural Product ID:  NPC125076
Common Name*:   Thiamine Chloride
IUPAC Name:   2-[3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethanol;chloride
Synonyms:   Betamin
Standard InCHIKey:  MYVIATVLJGTBFV-UHFFFAOYSA-M
Standard InCHI:  InChI=1S/C12H17N4OS.ClH/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15);1H/q+1;/p-1
SMILES:  Cc1c(CCO)sc[n+]1Cc1cnc(C)[nH]c1=N.[Cl-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1588
PubChem CID:   23423984
6042
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine derivatives
          • [CHEMONTID:0001285] Thiamines

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Seeds n.a. DOI[10.1002/(SICI)1097-0010(199909)79:12<1620::AID-JSFA410>3.0.CO;2-G]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-002-0656-1]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-015-2561-4]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2007.07.014]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.indcrop.2013.08.051]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.ssnmr.2006.05.001]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1080/09064710.2011.598543]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1365-2621.1989.tb04709.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1745-4530.2009.00507.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.15835/NBHA4017181]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.17221/540/2012-CJFS]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2137/145960607781635822]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2478/aoas-2014-0072]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3136/NSKKK.48.606]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3390/agriculture2030244]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[15563205]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Cornell Univeristy, Ithaca PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Petone, New Zealand PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Randolph, WI PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Shenandoah, IA PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Winslow, ME PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Cornell University, Geneva, NY PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Onehunga, New Zealand, PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Warminster, PA PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds n.a. PMID[17439238]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25026919]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25977015]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[26351516]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[26477735]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[27556441]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Aug PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Cracow, Poland 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Oct PMID[31206724]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. The ‘Dolina Mogilnicy’ Organic Farming Products Cooperative (Wolkowo, Poland) 2016-Oct PMID[31416184]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Fruits Wolkowo, Poland 2016-Oct PMID[31487816]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[31619015]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Flowers n.a. PMID[9301422]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[9301422]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25206 Cucurbita moschata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25206 Cucurbita moschata Species Cucurbitaceae 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 NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO441 NPC125076 n.a. Fruits 0.15 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.23 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.25 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.27 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.29 ± 0.02 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.34 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.42 ± 0.02 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.52 ± 0.02 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.54 ± 0.02 n.a. n.a. mg/100g of DM PMID[31487816]
NPO441 NPC125076 n.a. Fruits 0.60 ± 0.01 n.a. n.a. mg/100g of DM PMID[31487816]
NPO7269 NPC125076 n.a. Fruits 0.017-0.019 n.a. n.a. mg/100g DOI[10.3136/NSKKK.48.606]
NPO42046 NPC125076 n.a. Fruits 0.05 n.a. n.a. mg/100g PMID[31687561]
NPO25206 NPC125076 n.a. n.a. 0.20 ± 0.01 n.a. n.a. mg/100g of DM PMID[31416184]
NPO25206 NPC125076 n.a. n.a. 0.29 ± 0.01 n.a. n.a. mg/100g of DM PMID[31416184]
NPO25206 NPC125076 n.a. n.a. 0.33 ± 0.01c n.a. n.a. mg/100g of DM PMID[31416184]
NPO25206 NPC125076 n.a. n.a. 0.46 ± 0.02h n.a. n.a. mg/100g of DM PMID[31416184]
NPO25206 NPC125076 n.a. n.a. 0.62 ± 0.02k n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.15 ± 0.01b n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.15 ± 0.02b n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.24 ± 0.01f n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.26 ± 0.01d n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.33 ± 0.01c n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.33 ± 0.02c n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.39 ± 0.02e n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.56 ± 0.02 n.a. n.a. mg/100g of DM PMID[31416184]
NPO3938.2 NPC125076 n.a. n.a. 0.72 ± 0.03a n.a. n.a. mg/100g of DM PMID[31416184]
NPO42046 NPC125076 n.a. Seeds 0.034 n.a. n.a. mg/100g PMID[35684166]
NPO42046 NPC125076 n.a. Seeds 0.09 n.a. n.a. mg/32.25g PMID[35684166]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT55 Individual Protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 7943.3 nM PMID[496064]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 14581.0 nM PMID[496064]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 100000.0 nM PMID[496064]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 92.0 nM PMID[496064]
NPT159 Individual Protein Aberrant vpr protein Human immunodeficiency virus 1 Potency n.a. 56.2 nM PMID[496064]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Ki = 432000.0 nM PMID[496065]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Ki = 565000.0 nM PMID[496065]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Ki = 392000.0 nM PMID[496065]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Ki = 333000.0 nM PMID[496065]
NPT2 Others Unspecified Potency n.a. 23109.3 nM PMID[496064]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PMID[496064]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 10417.9 nM PMID[496064]
NPT2 Others Unspecified Kd = 0.122 nM PMID[496066]
NPT2 Others Unspecified Kd = 33.9 nM PMID[496066]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC125076 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC150950
1.0 High Similarity NPC189436
0.9167 High Similarity NPC329165
0.9098 High Similarity NPC320833
0.9098 High Similarity NPC317197
0.7581 Intermediate Similarity NPC162460

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC125076 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD807 Approved
1.0 High Similarity NPD808 Approved
0.7372 Intermediate Similarity NPD6121 Clinical (unspecified phase)
0.7152 Intermediate Similarity NPD3966 Clinical (unspecified phase)
0.6471 Remote Similarity NPD9402 Discontinued
0.6433 Remote Similarity NPD3876 Approved
0.6374 Remote Similarity NPD3877 Approved
0.6107 Remote Similarity NPD9104 Approved
0.5977 Remote Similarity NPD3333 Approved
0.5977 Remote Similarity NPD3332 Approved
0.596 Remote Similarity NPD1354 Approved
0.596 Remote Similarity NPD1355 Clinical (unspecified phase)
0.596 Remote Similarity NPD1356 Approved
0.5924 Remote Similarity NPD954 Phase 1
0.5766 Remote Similarity NPD2663 Approved
0.5737 Remote Similarity NPD3469 Phase 3
0.5714 Remote Similarity NPD6270 Approved
0.5699 Remote Similarity NPD3474 Discovery
0.5686 Remote Similarity NPD515 Phase 1
0.5632 Remote Similarity NPD1122 Clinical (unspecified phase)

  Bioactivity similarity: Similar Natural Products in NPASS

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