Structure

Physi-Chem Properties

Molecular Weight:  242.06
Volume:  241.737
LogP:  3.298
LogD:  2.848
LogS:  -3.621
# Rotatable Bonds:  1
TPSA:  59.67
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.666
Synthetic Accessibility Score:  2.004
Fsp3:  0.071
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.807
MDCK Permeability:  1.9019020328414626e-05
Pgp-inhibitor:  0.021
Pgp-substrate:  0.529
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.94

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.088
Plasma Protein Binding (PPB):  92.91307830810547%
Volume Distribution (VD):  0.641
Pgp-substrate:  8.912487983703613%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.934
CYP2C19-inhibitor:  0.864
CYP2C19-substrate:  0.15
CYP2C9-inhibitor:  0.718
CYP2C9-substrate:  0.945
CYP2D6-inhibitor:  0.774
CYP2D6-substrate:  0.914
CYP3A4-inhibitor:  0.564
CYP3A4-substrate:  0.23

ADMET: Excretion

Clearance (CL):  2.594
Half-life (T1/2):  0.387

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.155
Drug-inuced Liver Injury (DILI):  0.921
AMES Toxicity:  0.779
Rat Oral Acute Toxicity:  0.106
Maximum Recommended Daily Dose:  0.425
Skin Sensitization:  0.913
Carcinogencity:  0.864
Eye Corrosion:  0.251
Eye Irritation:  0.987
Respiratory Toxicity:  0.318

Download Data

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

  Natural Product: NPC108353

Natural Product ID:  NPC108353
Common Name*:   YYEBGEJSHOBJIB-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YYEBGEJSHOBJIB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H10O4/c1-17-8-5-6-11-9(7-8)14(16)13-10(15)3-2-4-12(13)18-11/h2-7,15H,1H3
SMILES:  COc1ccc2c(c1)c(=O)c1c(cccc1o2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12214329
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

*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
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[24216090]
NPO18656 Iphigenia indica Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18656 Iphigenia indica Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18656 Iphigenia indica Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18656 Iphigenia indica Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19688 Mangifera odorata Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27687 Peliosanthes sinica Species Asparagaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. PC50 = 42.7 uM PMID[510083]

☑ 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 NPC108353 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 NPC108353 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