Structure

Physi-Chem Properties

Molecular Weight:  236.13
Volume:  225.701
LogP:  -0.212
LogD:  -0.825
LogS:  -0.404
# Rotatable Bonds:  5
TPSA:  99.38
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.438
Synthetic Accessibility Score:  4.044
Fsp3:  1.0
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:  -5.104
MDCK Permeability:  0.0002829823351930827
Pgp-inhibitor:  0.001
Pgp-substrate:  0.546
Human Intestinal Absorption (HIA):  0.264
20% Bioavailability (F20%):  0.838
30% Bioavailability (F30%):  0.051

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.317
Plasma Protein Binding (PPB):  28.105892181396484%
Volume Distribution (VD):  0.632
Pgp-substrate:  60.43693542480469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.019
CYP1A2-substrate:  0.318
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.596
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.046

ADMET: Excretion

Clearance (CL):  5.055
Half-life (T1/2):  0.75

ADMET: Toxicity

hERG Blockers:  0.096
Human Hepatotoxicity (H-HT):  0.058
Drug-inuced Liver Injury (DILI):  0.182
AMES Toxicity:  0.287
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.586
Carcinogencity:  0.034
Eye Corrosion:  0.004
Eye Irritation:  0.331
Respiratory Toxicity:  0.033

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC233651

Natural Product ID:  NPC233651
Common Name*:   NAJPAGUETSZHOG-DOLQZWNJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NAJPAGUETSZHOG-DOLQZWNJSA-N
Standard InCHI:  InChI=1S/C10H20O6/c1-2-3-4-15-10(6-11)9(14)8(13)7(12)5-16-10/h7-9,11-14H,2-6H2,1H3/t7-,8-,9+,10-/m1/s1
SMILES:  CCCCO[C@@]1(CO)[C@H]([C@@H]([C@@H](CO1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   50914217
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001656] Acetals
            • [CHEMONTID:0004472] Ketals

*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
NPO4562 Lonchocarpus urucu Species Fabaceae Eukaryota n.a. root n.a. PMID[10075742]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. PMID[11430011]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[19615910]
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]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[21465337]
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 n.a. Konya, Turkey 2007-APR PMID[24901948]
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 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]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[29323912]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO9740 Dacrycarpus imbricatus Species Podocarpaceae Eukaryota Twigs n.a. n.a. PMID[32786878]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[731398]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[731398]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6017 Artemisia arbuscula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9740 Dacrycarpus imbricatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6017 Artemisia arbuscula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28033 Trididemnum cyclops Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6017 Artemisia arbuscula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28084 Aspergillus panamensis Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4562 Lonchocarpus urucu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13443 Doris montereyensis Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27769 Annona ambotay Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6559 Duddingtonia flagrans Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9094 Citrus reshni Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8794 Aconitum fauriei Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO182 Cylas formicarius Species Brentidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28630 Myrocarpus frondosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28349 Eria pubescens Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO378 Myristica argentea Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO790 Cybister confusus Species Dytiscidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2622 Cheilanthes mysurensis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9234 Cynoctonum wilfordii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1477 Egregia menziesii Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9740 Dacrycarpus imbricatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28687 Cladosiphon decipiens Species Chordariaceae 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

☑ 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

☑ 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 NPC233651 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

  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 NPC233651 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

  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