Structure

Physi-Chem Properties

Molecular Weight:  183.16
Volume:  201.486
LogP:  1.509
LogD:  2.164
LogS:  -1.114
# Rotatable Bonds:  0
TPSA:  23.47
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.61
Synthetic Accessibility Score:  4.245
Fsp3:  1.0
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:  -4.699
MDCK Permeability:  1.6730828065192327e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.966
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.019
30% Bioavailability (F30%):  0.689

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.858
Plasma Protein Binding (PPB):  14.768163681030273%
Volume Distribution (VD):  2.373
Pgp-substrate:  73.3100814819336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.177
CYP1A2-substrate:  0.453
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.958
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.229
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.864
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.627

ADMET: Excretion

Clearance (CL):  13.646
Half-life (T1/2):  0.688

ADMET: Toxicity

hERG Blockers:  0.109
Human Hepatotoxicity (H-HT):  0.346
Drug-inuced Liver Injury (DILI):  0.616
AMES Toxicity:  0.036
Rat Oral Acute Toxicity:  0.902
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.747
Carcinogencity:  0.156
Eye Corrosion:  0.994
Eye Irritation:  0.339
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC221489

Natural Product ID:  NPC221489
Common Name*:   MDEHQFAHARLWSP-ISUQUUIWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MDEHQFAHARLWSP-ISUQUUIWSA-N
Standard InCHI:  InChI=1S/C11H21NO/c1-7-5-12(3)6-10-8(2)11(13)4-9(7)10/h7-11,13H,4-6H2,1-3H3/t7-,8-,9-,10-,11-/m1/s1
SMILES:  C[C@@H]1CN(C)C[C@@H]2[C@@H](C)[C@@H](C[C@H]12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   133618335
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines

*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
NPO11944 Incarvillea sinensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[10514316]
NPO9878 Dichapetalum gelonioides Species Dichapetalaceae Eukaryota stem bark Philippines n.a. PMID[16562829]
NPO12054 Holostylis reniformis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[17438049]
NPO12054 Holostylis reniformis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[20961092]
NPO915 Xylaria polymorpha Species Xylariaceae Eukaryota n.a. fruit body n.a. PMID[21942847]
NPO9878 Dichapetalum gelonioides Species Dichapetalaceae Eukaryota n.a. n.a. n.a. PMID[24597894]
NPO20351 Emericella variecolor Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26394166]
NPO7492 Mucuna birdwoodiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11308 Rohdea japonica Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11944 Incarvillea sinensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20351 Emericella variecolor Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11944 Incarvillea sinensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11308 Rohdea japonica Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7492 Mucuna birdwoodiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12054 Holostylis reniformis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7109 Eugenia edulis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20351 Emericella variecolor Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2349 Picrasma excelsa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11470 Sorghum caudatum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12281 Aleurodiscus amorphus Species Stereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7492 Mucuna birdwoodiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11308 Rohdea japonica Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4845 Arachniodes standishii Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3700 Frasera speciosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12165 Comanthosphace japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11944 Incarvillea sinensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO622 Stictina crocata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO915 Xylaria polymorpha Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11829 Acacia ehrenbergiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7109 Eugenia edulis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11139 Godmania aesculifolia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4988 Lavandula stoechas Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9878 Dichapetalum gelonioides Species Dichapetalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6900 Koenigia divaricata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6055 Enkianthus cernuus Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5294 Stemona ovata Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12054 Holostylis reniformis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8150 Calibrachoa parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5715 Hyalodendriella betulae Species n.a. 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 NPC221489 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 NPC221489 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