Structure

Physi-Chem Properties

Molecular Weight:  296.07
Volume:  285.302
LogP:  4.145
LogD:  3.604
LogS:  -6.545
# Rotatable Bonds:  1
TPSA:  50.06
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.685
Synthetic Accessibility Score:  2.51
Fsp3:  0.176
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.972
MDCK Permeability:  5.017943476559594e-05
Pgp-inhibitor:  0.778
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.08
Plasma Protein Binding (PPB):  95.82760620117188%
Volume Distribution (VD):  0.82
Pgp-substrate:  3.7681772708892822%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.734
CYP2C19-inhibitor:  0.969
CYP2C19-substrate:  0.163
CYP2C9-inhibitor:  0.765
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.91
CYP2D6-substrate:  0.943
CYP3A4-inhibitor:  0.924
CYP3A4-substrate:  0.164

ADMET: Excretion

Clearance (CL):  15.054
Half-life (T1/2):  0.167

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.805
Drug-inuced Liver Injury (DILI):  0.962
AMES Toxicity:  0.873
Rat Oral Acute Toxicity:  0.174
Maximum Recommended Daily Dose:  0.612
Skin Sensitization:  0.134
Carcinogencity:  0.919
Eye Corrosion:  0.004
Eye Irritation:  0.273
Respiratory Toxicity:  0.746

Download Data

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

  Natural Product: NPC144312

Natural Product ID:  NPC144312
Common Name*:   XWTCRKNSJARUIU-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XWTCRKNSJARUIU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H12O5/c1-18-9-2-3-10-13(4-9)19-7-12-11-5-15-16(21-8-20-15)6-14(11)22-17(10)12/h2-6H,7-8H2,1H3
SMILES:  COc1ccc2-c3c(COc2c1)c1cc2c(cc1o3)OCO2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11822566
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002617] Furanoisoflavonoids
          • [CHEMONTID:0001608] Pterocarpans

*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
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. stem n.a. DOI[10.1016/S0031-9422(99)00103-X]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19969457]
NPO5885 Bathymodiolus thermophilus Species Mytilidae Eukaryota n.a. gill n.a. PMID[21222464]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21314138]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25708 Erioderma phaeorhizum Species Pannariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24229 Schoenus nigricans Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5753 Glycosmis montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25052 Diphysa robinioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25730 Prorhinotermes simplex Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5885 Bathymodiolus thermophilus Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24691 Astragalus orbiculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5368 Achillea cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25533 Stellaster equestris Species Goniasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12750 Cordia americana Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25758 Aspergillus amstelodami Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25149 Centaurea arguta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6147 Eupatorium riparium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2671 Pedicularis semitorta Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24128 Cassinia longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21669 Acacia sieberana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25422 Artemisia dracunculoides 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 NPC144312 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 NPC144312 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