Structure

Physi-Chem Properties

Molecular Weight:  342.11
Volume:  331.32
LogP:  2.694
LogD:  2.854
LogS:  -4.453
# Rotatable Bonds:  2
TPSA:  77.38
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.817
Synthetic Accessibility Score:  3.81
Fsp3:  0.368
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.787
MDCK Permeability:  2.031957956205588e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.018
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.016
Plasma Protein Binding (PPB):  95.89148712158203%
Volume Distribution (VD):  0.696
Pgp-substrate:  5.6675028800964355%

ADMET: Metabolism

CYP1A2-inhibitor:  0.317
CYP1A2-substrate:  0.533
CYP2C19-inhibitor:  0.346
CYP2C19-substrate:  0.108
CYP2C9-inhibitor:  0.559
CYP2C9-substrate:  0.537
CYP2D6-inhibitor:  0.904
CYP2D6-substrate:  0.602
CYP3A4-inhibitor:  0.682
CYP3A4-substrate:  0.262

ADMET: Excretion

Clearance (CL):  17.801
Half-life (T1/2):  0.47

ADMET: Toxicity

hERG Blockers:  0.15
Human Hepatotoxicity (H-HT):  0.27
Drug-inuced Liver Injury (DILI):  0.693
AMES Toxicity:  0.434
Rat Oral Acute Toxicity:  0.193
Maximum Recommended Daily Dose:  0.804
Skin Sensitization:  0.949
Carcinogencity:  0.732
Eye Corrosion:  0.004
Eye Irritation:  0.925
Respiratory Toxicity:  0.635

Download Data

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

  Natural Product: NPC158840

Natural Product ID:  NPC158840
Common Name*:   CGEORJKFOZSMEZ-WXPXUSHHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CGEORJKFOZSMEZ-WXPXUSHHSA-N
Standard InCHI:  InChI=1S/C19H18O6/c20-14-3-1-10(5-15(14)21)18-12-7-23-19(13(12)8-22-18)11-2-4-16-17(6-11)25-9-24-16/h1-6,12-13,18-21H,7-9H2/t12-,13-,18+,19-/m0/s1
SMILES:  c1cc(c(cc1[C@@H]1[C@H]2CO[C@@H](c3ccc4c(c3)OCO4)[C@H]2CO1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   46917405
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans

*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
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. PMID[15387676]
NPO16877 Aconitum episcopale Species Ranunculaceae Eukaryota n.a. root n.a. PMID[21417277]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[22365754]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[27329938]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[33296199]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9962 Pocillopora damicornis Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13926 Protaetia cuprea Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3741 Pagrus major Species Sparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16552 Aromia moschata Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7909 Parmelia vittata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15193 Cacia concinna n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16877 Aconitum episcopale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16119 Eucalyptus hybrid Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO745 Rubus trifidus Species Rosaceae 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
NPT213 Individual Protein Cytochrome P450 2C19 Homo sapiens Kcat = 15.0 /min PMID[548213]
NPT213 Individual Protein Cytochrome P450 2C19 Homo sapiens Km = 7300.0 nM PMID[548213]
NPT213 Individual Protein Cytochrome P450 2C19 Homo sapiens Drug metabolism = 9.4 nmol/min PMID[548213]
NPT208 Individual Protein Cytochrome P450 1A2 Homo sapiens Drug metabolism = 0.38 nmol/min PMID[548213]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens Drug metabolism = 0.19 nmol/min PMID[548213]
NPT3150 Individual Protein Catechol O-methyltransferase Rattus norvegicus Vmax = 3.2 nmol/min PMID[548213]
NPT3150 Individual Protein Catechol O-methyltransferase Rattus norvegicus Km = 7700.0 nM PMID[548213]
NPT4546 Individual Protein Catechol O-methyltransferase Homo sapiens Vmax = 0.59 nmol/min PMID[548213]
NPT4546 Individual Protein Catechol O-methyltransferase Homo sapiens Km = 2400.0 nM PMID[548213]
NPT27 Others Unspecified Km = 16800.0 nM PMID[548213]
NPT27 Others Unspecified Vmax = 4.4 nmol/min PMID[548213]
NPT27 Others Unspecified Vmax = 1.9 nmol/min PMID[548213]
NPT27 Others Unspecified Km = 2900.0 nM PMID[548213]
NPT27 Others Unspecified Vmax = 0.55 nmol/min PMID[548213]
NPT27 Others Unspecified Vmax = 0.28 nmol/min PMID[548213]
NPT27 Others Unspecified Km = 4100.0 nM PMID[548213]
NPT27 Others Unspecified Km = 9900.0 nM PMID[548213]

☑ 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 NPC158840 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 NPC158840 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