Structure

Physi-Chem Properties

Molecular Weight:  233.07
Volume:  223.414
LogP:  2.732
LogD:  3.052
LogS:  -3.505
# Rotatable Bonds:  2
TPSA:  49.81
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.793
Synthetic Accessibility Score:  2.507
Fsp3:  0.25
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:  -4.566
MDCK Permeability:  2.6189289201283827e-05
Pgp-inhibitor:  0.088
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.242
Plasma Protein Binding (PPB):  95.56842041015625%
Volume Distribution (VD):  0.659
Pgp-substrate:  4.038809776306152%

ADMET: Metabolism

CYP1A2-inhibitor:  0.994
CYP1A2-substrate:  0.891
CYP2C19-inhibitor:  0.897
CYP2C19-substrate:  0.739
CYP2C9-inhibitor:  0.344
CYP2C9-substrate:  0.91
CYP2D6-inhibitor:  0.806
CYP2D6-substrate:  0.92
CYP3A4-inhibitor:  0.911
CYP3A4-substrate:  0.332

ADMET: Excretion

Clearance (CL):  11.659
Half-life (T1/2):  0.349

ADMET: Toxicity

hERG Blockers:  0.063
Human Hepatotoxicity (H-HT):  0.153
Drug-inuced Liver Injury (DILI):  0.818
AMES Toxicity:  0.723
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.239
Skin Sensitization:  0.756
Carcinogencity:  0.919
Eye Corrosion:  0.005
Eye Irritation:  0.385
Respiratory Toxicity:  0.763

Download Data

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

  Natural Product: NPC65247

Natural Product ID:  NPC65247
Common Name*:   JOYNNZYGFVXVEZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JOYNNZYGFVXVEZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H11NO4/c1-14-7-3-4-8-9(5-7)13-12-11(10(8)15-2)16-6-17-12/h3-5H,6H2,1-2H3
SMILES:  COc1ccc2c(c1)nc1c(c2OC)OCO1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10775978
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines and derivatives

*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
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[11170656]
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. Suriname rainforest n.a. PMID[11170656]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8394 Ramalina geniculata Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26672 Matricaria tenuifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24789 Opuntia elatior Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25724 Mya arenaria Species Myidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25987 Euphorbia obtusifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26734 Cupaniopsis azantha Species Sapindaceae 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 NPC65247 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 NPC65247 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