Structure

Physi-Chem Properties

Molecular Weight:  346.14
Volume:  348.433
LogP:  3.473
LogD:  3.191
LogS:  -3.885
# Rotatable Bonds:  4
TPSA:  85.97
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.679
Synthetic Accessibility Score:  3.573
Fsp3:  0.474
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:  -4.732
MDCK Permeability:  2.7277606932329945e-05
Pgp-inhibitor:  0.168
Pgp-substrate:  0.07
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.122
Plasma Protein Binding (PPB):  87.29833221435547%
Volume Distribution (VD):  1.028
Pgp-substrate:  11.724119186401367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.422
CYP1A2-substrate:  0.554
CYP2C19-inhibitor:  0.595
CYP2C19-substrate:  0.3
CYP2C9-inhibitor:  0.687
CYP2C9-substrate:  0.873
CYP2D6-inhibitor:  0.159
CYP2D6-substrate:  0.126
CYP3A4-inhibitor:  0.175
CYP3A4-substrate:  0.34

ADMET: Excretion

Clearance (CL):  10.607
Half-life (T1/2):  0.626

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.962
Drug-inuced Liver Injury (DILI):  0.944
AMES Toxicity:  0.067
Rat Oral Acute Toxicity:  0.234
Maximum Recommended Daily Dose:  0.082
Skin Sensitization:  0.086
Carcinogencity:  0.882
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC173381

Natural Product ID:  NPC173381
Common Name*:   GWZZKJQYTUFZHD-FUHWJXTLSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GWZZKJQYTUFZHD-FUHWJXTLSA-N
Standard InCHI:  InChI=1S/C19H22O6/c1-10(2)9-14(21)24-18-16(22)15-12(25-19(18,3)4)7-5-11-6-8-13(20)23-17(11)15/h5-8,10,16,18,22H,9H2,1-4H3/t16-,18+/m0/s1
SMILES:  CC(C)CC(=O)O[C@@H]1[C@H](c2c(ccc3ccc(=O)oc23)OC1(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14055879
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0003484] Pyranocoumarins
          • [CHEMONTID:0003485] Angular pyranocoumarins

*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
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. whole plant n.a. PMID[16079548]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota stems n.a. n.a. PMID[19754130]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. leaf n.a. PMID[24024688]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. fruit n.a. PMID[25522543]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. PMID[7798960]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4311 Asterolasia squamuligera Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11107 Stevia alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7263 Phyllobates aurotaenia Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29494 Stoeba extensa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7003 Streptomyces violaceochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10402 Strophanthus eminii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9919 Jaspis stellifera Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9765 Petriella guttulata Species Microascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17324 Pluchea dioscoridis Species Asteraceae 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 NPC173381 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 NPC173381 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