Structure

Physi-Chem Properties

Molecular Weight:  147.1
Volume:  167.491
LogP:  2.752
LogD:  2.209
LogS:  -1.765
# Rotatable Bonds:  0
TPSA:  12.89
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.549
Synthetic Accessibility Score:  3.213
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.497
MDCK Permeability:  2.5987579647335224e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.952
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.965
Plasma Protein Binding (PPB):  72.18215942382812%
Volume Distribution (VD):  1.58
Pgp-substrate:  24.357696533203125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.922
CYP1A2-substrate:  0.918
CYP2C19-inhibitor:  0.48
CYP2C19-substrate:  0.859
CYP2C9-inhibitor:  0.176
CYP2C9-substrate:  0.808
CYP2D6-inhibitor:  0.046
CYP2D6-substrate:  0.899
CYP3A4-inhibitor:  0.742
CYP3A4-substrate:  0.559

ADMET: Excretion

Clearance (CL):  13.417
Half-life (T1/2):  0.634

ADMET: Toxicity

hERG Blockers:  0.089
Human Hepatotoxicity (H-HT):  0.558
Drug-inuced Liver Injury (DILI):  0.277
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.618
Maximum Recommended Daily Dose:  0.952
Skin Sensitization:  0.868
Carcinogencity:  0.384
Eye Corrosion:  0.11
Eye Irritation:  0.714
Respiratory Toxicity:  0.9

Download Data

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

  Natural Product: NPC47920

Natural Product ID:  NPC47920
Common Name*:   ZHQQRIUYLMXDPP-ZETCQYMHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZHQQRIUYLMXDPP-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C10H13N/c1-7-3-4-9-8(2)5-11-6-10(7)9/h5-7H,3-4H2,1-2H3/t7-/m0/s1
SMILES:  C[C@H]1CCc2c(C)cncc12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   68231
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0004152] Methylpyridines

*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
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota roots n.a. n.a. PMID[12398547]
NPO26990 Rhizochalina incrustata n.a. n.a. n.a. n.a. n.a. n.a. PMID[15730256]
NPO25801 Harungana madagascariensis Species Hypericaceae Eukaryota stem bark n.a. n.a. PMID[16499321]
NPO25801 Harungana madagascariensis Species Hypericaceae Eukaryota Leaves n.a. n.a. PMID[17352491]
NPO26990 Rhizochalina incrustata n.a. n.a. n.a. n.a. n.a. n.a. PMID[18052325]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[18164718]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. root n.a. PMID[18481026]
NPO2937 Pseudoalteromonas rubra Species Pseudoalteromonadaceae Bacteria n.a. n.a. n.a. PMID[18922034]
NPO26547 Uncaria tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[1919590]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. root n.a. PMID[19336935]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO26547 Uncaria tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[2553871]
NPO25801 Harungana madagascariensis Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[26727375]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[28485933]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. n.a. n.a. PMID[32315181]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[547813]
NPO20123 Actinidia polygama Species Actinidiaceae Eukaryota n.a. n.a. n.a. PMID[6061704]
NPO26547 Uncaria tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20123 Actinidia polygama Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20123 Actinidia polygama Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25801 Harungana madagascariensis Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26547 Uncaria tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20123 Actinidia polygama Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26547 Uncaria tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26815 Asteracantha longifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26333 Actinidia arguta Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20123 Actinidia polygama Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26990 Rhizochalina incrustata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27153 Vasconcellea cundinamarcensis Species Caricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26415 Polyporus anthracophilus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2937 Pseudoalteromonas rubra Species Pseudoalteromonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14566 Delphinium fangshanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28220 Streptomyces goshikiensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25801 Harungana madagascariensis Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26492 Sesamoides canescens Species Resedaceae 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 NPC47920 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 NPC47920 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