Structure

Physi-Chem Properties

Molecular Weight:  286.11
Volume:  269.914
LogP:  -0.916
LogD:  -1.012
LogS:  -1.282
# Rotatable Bonds:  4
TPSA:  119.61
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  3.321
Fsp3:  0.538
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:  -5.512
MDCK Permeability:  4.155841816100292e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.141
Human Intestinal Absorption (HIA):  0.637
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.316
Plasma Protein Binding (PPB):  31.578258514404297%
Volume Distribution (VD):  0.388
Pgp-substrate:  50.8230094909668%

ADMET: Metabolism

CYP1A2-inhibitor:  0.105
CYP1A2-substrate:  0.036
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.43
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.138
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.323
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.045

ADMET: Excretion

Clearance (CL):  1.474
Half-life (T1/2):  0.792

ADMET: Toxicity

hERG Blockers:  0.133
Human Hepatotoxicity (H-HT):  0.025
Drug-inuced Liver Injury (DILI):  0.277
AMES Toxicity:  0.204
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.394
Carcinogencity:  0.321
Eye Corrosion:  0.004
Eye Irritation:  0.724
Respiratory Toxicity:  0.022

Download Data

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

  Natural Product: NPC94366

Natural Product ID:  NPC94366
Common Name*:   PUQSUZTXKPLAPR-SYLRKERUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PUQSUZTXKPLAPR-SYLRKERUSA-N
Standard InCHI:  InChI=1S/C13H18O7/c14-5-7-1-3-8(4-2-7)19-13-12(18)11(17)10(16)9(6-15)20-13/h1-4,9-18H,5-6H2/t9-,10-,11-,12-,13-/m1/s1
SMILES:  c1cc(ccc1CO)O[C@H]1[C@@H]([C@@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15976294
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:0004165] Phenolic glycosides

*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
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. tuber n.a. PMID[15180301]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[17381154]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. seed n.a. PMID[21049975]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. aerial part n.a. PMID[25154406]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[25843525]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22309 Gastrodia elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21460 Anethum graveolens Species Apiaceae 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 NPC94366 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 NPC94366 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