Structure

Physi-Chem Properties

Molecular Weight:  165.12
Volume:  184.837
LogP:  1.146
LogD:  1.205
LogS:  -0.362
# Rotatable Bonds:  3
TPSA:  32.26
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.708
Synthetic Accessibility Score:  2.567
Fsp3:  0.4
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:  -4.811
MDCK Permeability:  3.1189269066089764e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.251
Plasma Protein Binding (PPB):  10.764822006225586%
Volume Distribution (VD):  3.09
Pgp-substrate:  81.02647399902344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.135
CYP1A2-substrate:  0.312
CYP2C19-inhibitor:  0.042
CYP2C19-substrate:  0.902
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.178
CYP2D6-inhibitor:  0.435
CYP2D6-substrate:  0.852
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.446

ADMET: Excretion

Clearance (CL):  10.282
Half-life (T1/2):  0.402

ADMET: Toxicity

hERG Blockers:  0.053
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.508
Maximum Recommended Daily Dose:  0.513
Skin Sensitization:  0.097
Carcinogencity:  0.035
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.803

Download Data

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

  Natural Product: NPC304078

Natural Product ID:  NPC304078
Common Name*:   KWGRBVOPPLSCSI-LHIURRSHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KWGRBVOPPLSCSI-LHIURRSHSA-N
Standard InCHI:  InChI=1S/C10H15NO/c1-8(11-2)10(12)9-6-4-3-5-7-9/h3-8,10-12H,1-2H3/t8?,10-/m1/s1
SMILES:  CC([C@H](c1ccccc1)O)NC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11972440
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0002811] Phenylpropanes

*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
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[21465337]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO9315 Ephedra likiangensis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12238 Ephedra lepidosperma Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20722 Ephedra przewalskii Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18715.1 Ephedra minuta var. dioeca Varieties Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22155 Ephedra saxatilis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507.1 Ephedra intermedia var. tibetica Varieties Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12705 Ephedra monosperma Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23538 Ephedra distachya Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31194 Ephedra procera Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7976 Ephedra gerardiana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27206 Ephedra tweediana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20178 Ephedra regeliana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9315 Ephedra likiangensis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20178 Ephedra regeliana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7976 Ephedra gerardiana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18715.1 Ephedra minuta var. dioeca Varieties Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18085.1 Ephedra major subsp. procera Subspecies Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23538 Ephedra distachya Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507.1 Ephedra intermedia var. tibetica Varieties Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12705 Ephedra monosperma Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27206 Ephedra tweediana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12238 Ephedra lepidosperma Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22155 Ephedra saxatilis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20722 Ephedra przewalskii Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7976 Ephedra gerardiana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23538 Ephedra distachya Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9315 Ephedra likiangensis Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23538 Ephedra distachya Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12705 Ephedra monosperma Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7976 Ephedra gerardiana Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7450 Sida acuta Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae 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 NPC304078 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 NPC304078 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