Structure

Physi-Chem Properties

Molecular Weight:  268.09
Volume:  264.407
LogP:  1.138
LogD:  0.56
LogS:  -1.353
# Rotatable Bonds:  7
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.507
Synthetic Accessibility Score:  2.653
Fsp3:  0.308
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.236
MDCK Permeability:  1.418596275470918e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.844
Human Intestinal Absorption (HIA):  0.055
20% Bioavailability (F20%):  0.78
30% Bioavailability (F30%):  0.758

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.854
Plasma Protein Binding (PPB):  79.27411651611328%
Volume Distribution (VD):  0.461
Pgp-substrate:  24.369121551513672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.527
CYP1A2-substrate:  0.144
CYP2C19-inhibitor:  0.064
CYP2C19-substrate:  0.443
CYP2C9-inhibitor:  0.052
CYP2C9-substrate:  0.622
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.513
CYP3A4-inhibitor:  0.048
CYP3A4-substrate:  0.284

ADMET: Excretion

Clearance (CL):  8.779
Half-life (T1/2):  0.929

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.161
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.172
Rat Oral Acute Toxicity:  0.311
Maximum Recommended Daily Dose:  0.506
Skin Sensitization:  0.885
Carcinogencity:  0.452
Eye Corrosion:  0.003
Eye Irritation:  0.056
Respiratory Toxicity:  0.154

Download Data

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

  Natural Product: NPC216217

Natural Product ID:  NPC216217
Common Name*:   QXRAHTFDPBQKIM-SNVBAGLBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QXRAHTFDPBQKIM-SNVBAGLBSA-N
Standard InCHI:  InChI=1S/C13H16O6/c1-18-12-6-9(2-4-11(12)16)3-5-13(17)19-8-10(15)7-14/h2-6,10,14-16H,7-8H2,1H3/t10-/m1/s1
SMILES:  COc1cc(ccc1O)C=CC(=O)OC[C@@H](CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives
          • [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[14510614]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. stem n.a. PMID[21443171]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12731 Porodaedalea pini Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24684 Eremanthus crotonoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2617 Dracocephalum multicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14889 Vachellia farnesiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23423 Phellopterus littoralis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24716 Pulvinula constellatio Species Pyronemataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19677 Cephalaria transsylvanica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22021 Teucrium spinosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25027 Cynoglossum creticum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23283 Triptilion benaventei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21168 Erylus lendenfeldi Species Geodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22352 Lysimachia heterogenea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23737 Allium turcomanicum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24110 Lippia alba Species Verbenaceae 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 NPC216217 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 NPC216217 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