Structure

Physi-Chem Properties

Molecular Weight:  230.13
Volume:  255.281
LogP:  4.206
LogD:  4.26
LogS:  -4.63
# Rotatable Bonds:  4
TPSA:  26.28
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.735
Synthetic Accessibility Score:  3.258
Fsp3:  0.333
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:  -4.667
MDCK Permeability:  3.1383457098854706e-05
Pgp-inhibitor:  0.161
Pgp-substrate:  0.05
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.078
Plasma Protein Binding (PPB):  97.17317962646484%
Volume Distribution (VD):  1.384
Pgp-substrate:  1.2976362705230713%

ADMET: Metabolism

CYP1A2-inhibitor:  0.821
CYP1A2-substrate:  0.81
CYP2C19-inhibitor:  0.941
CYP2C19-substrate:  0.231
CYP2C9-inhibitor:  0.849
CYP2C9-substrate:  0.524
CYP2D6-inhibitor:  0.425
CYP2D6-substrate:  0.881
CYP3A4-inhibitor:  0.534
CYP3A4-substrate:  0.413

ADMET: Excretion

Clearance (CL):  9.621
Half-life (T1/2):  0.599

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.273
Drug-inuced Liver Injury (DILI):  0.802
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.221
Maximum Recommended Daily Dose:  0.224
Skin Sensitization:  0.053
Carcinogencity:  0.175
Eye Corrosion:  0.006
Eye Irritation:  0.064
Respiratory Toxicity:  0.43

Download Data

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

  Natural Product: NPC214724

Natural Product ID:  NPC214724
Common Name*:   KATZGWUZXSGURX-NYYWCZLTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KATZGWUZXSGURX-NYYWCZLTSA-N
Standard InCHI:  InChI=1S/C15H18O2/c1-11(8-14-9-12(2)10-17-14)4-5-15-13(3)6-7-16-15/h4,6-7,9-10H,5,8H2,1-3H3/b11-4+
SMILES:  C/C(=CCc1c(C)cco1)/Cc1cc(C)co1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5372204
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004144] Heteroaromatic compounds

*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
NPO2324 Phoma herbarum Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[12713403]
NPO16241 Eucalyptus perriniana Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[23980409]
NPO16722 Tolypothrix nodosa Species Tolypothrichaceae Bacteria n.a. n.a. n.a. PMID[8792625]
NPO16722 Tolypothrix nodosa Species Tolypothrichaceae Bacteria n.a. n.a. n.a. PMID[9748382]
NPO16587 Actinodaphne longifolia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15419 Tunica prolifera n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17084 Marsilea quadrifolia Species Marsileaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15935 Pinus parviflora Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16241 Eucalyptus perriniana Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13829 Cryptocarya angulata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10869 Cota saguramica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17389 Papilio xuthus Species Papilionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17015 Plantago hookeriana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17537 Anthotroche blackii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14831 Mastophora hutchinsoni Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10282 Solenostoma triste Species Solenostomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16722 Tolypothrix nodosa Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2324 Phoma herbarum Species Didymellaceae 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 NPC214724 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 NPC214724 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