Structure

Physi-Chem Properties

Molecular Weight:  300.06
Volume:  291.273
LogP:  2.444
LogD:  2.169
LogS:  -3.48
# Rotatable Bonds:  2
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.582
Synthetic Accessibility Score:  2.56
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.027
MDCK Permeability:  1.852480272646062e-05
Pgp-inhibitor:  0.138
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.489
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.055
Plasma Protein Binding (PPB):  99.4452133178711%
Volume Distribution (VD):  0.45
Pgp-substrate:  2.081075429916382%

ADMET: Metabolism

CYP1A2-inhibitor:  0.947
CYP1A2-substrate:  0.306
CYP2C19-inhibitor:  0.171
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.606
CYP2C9-substrate:  0.437
CYP2D6-inhibitor:  0.216
CYP2D6-substrate:  0.241
CYP3A4-inhibitor:  0.495
CYP3A4-substrate:  0.198

ADMET: Excretion

Clearance (CL):  8.579
Half-life (T1/2):  0.893

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.179
Drug-inuced Liver Injury (DILI):  0.546
AMES Toxicity:  0.61
Rat Oral Acute Toxicity:  0.961
Maximum Recommended Daily Dose:  0.916
Skin Sensitization:  0.927
Carcinogencity:  0.747
Eye Corrosion:  0.004
Eye Irritation:  0.937
Respiratory Toxicity:  0.279

Download Data

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

  Natural Product: NPC233724

Natural Product ID:  NPC233724
Common Name*:   PFRGTMTYWMVLMU-QPEQYQDCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PFRGTMTYWMVLMU-QPEQYQDCSA-N
Standard InCHI:  InChI=1S/C16H12O6/c1-21-16-11(18)5-3-9-14(20)13(22-15(9)16)7-8-2-4-10(17)12(19)6-8/h2-7,17-19H,1H3/b13-7-
SMILES:  COc1c(ccc2C(=O)/C(=C/c3ccc(c(c3)O)O)/Oc12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5281257
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0001631] Aurone flavonoids

*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
NPO1707 Coreopsis lanceolata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24236492]
NPO1707 Coreopsis lanceolata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1707 Coreopsis lanceolata 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
NPT35 Others n.a. Retention_time = 25.04 min PMID[505367]

☑ 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 NPC233724 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 NPC233724 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