Structure

Physi-Chem Properties

Molecular Weight:  287.15
Volume:  295.184
LogP:  1.389
LogD:  0.952
LogS:  -1.243
# Rotatable Bonds:  1
TPSA:  41.93
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.801
Synthetic Accessibility Score:  4.227
Fsp3:  0.529
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:  -4.584
MDCK Permeability:  1.9968345441156998e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.04
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  19.520984649658203%
Volume Distribution (VD):  2.767
Pgp-substrate:  73.98881530761719%

ADMET: Metabolism

CYP1A2-inhibitor:  0.09
CYP1A2-substrate:  0.882
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.951
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.397
CYP2D6-inhibitor:  0.906
CYP2D6-substrate:  0.922
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.873

ADMET: Excretion

Clearance (CL):  4.169
Half-life (T1/2):  0.54

ADMET: Toxicity

hERG Blockers:  0.248
Human Hepatotoxicity (H-HT):  0.319
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.634
Maximum Recommended Daily Dose:  0.879
Skin Sensitization:  0.788
Carcinogencity:  0.092
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.963

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC139478

Natural Product ID:  NPC139478
Common Name*:   QORVDGQLPPAFRS-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QORVDGQLPPAFRS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H21NO3.BrH/c1-18-8-7-17-6-5-12(19)9-14(17)21-16-13(20-2)4-3-11(10-18)15(16)17;/h3-6,12,14,19H,7-10H2,1-2H3;1H
SMILES:  CN1CCC23C=CC(CC2Oc2c(ccc(C1)c32)OC)O.Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21946319
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001775] Amaryllidaceae alkaloids
        • [CHEMONTID:0004128] Galanthamine-type amaryllidaceae alkaloids

*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
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[15930771]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18356045]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. Turkey n.a. PMID[19299148]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. stem n.a. PMID[20066175]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[21510636]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25061748]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9942.1 Narcissus tazetta var. chinensis Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9074 Narcissus papyraceus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7280 Lycoris squamigera Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1598 Leucojum vernum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9942.1 Narcissus tazetta var. chinensis Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1598 Leucojum vernum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9074 Narcissus papyraceus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7280 Lycoris squamigera Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9074 Narcissus papyraceus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1598 Leucojum vernum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7280 Lycoris squamigera Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25694 Leucojum aestivum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19673 Galanthus nivalis Species Amaryllidaceae 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 NPC139478 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 NPC139478 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