Structure

Physi-Chem Properties

Molecular Weight:  320.2
Volume:  339.862
LogP:  4.183
LogD:  3.48
LogS:  -3.224
# Rotatable Bonds:  2
TPSA:  35.16
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.78
Synthetic Accessibility Score:  2.305
Fsp3:  0.45
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:  -4.919
MDCK Permeability:  1.0999435289704707e-05
Pgp-inhibitor:  0.756
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.04
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  85.7568359375%
Volume Distribution (VD):  2.579
Pgp-substrate:  12.607487678527832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.544
CYP1A2-substrate:  0.945
CYP2C19-inhibitor:  0.092
CYP2C19-substrate:  0.826
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.044
CYP2D6-inhibitor:  0.964
CYP2D6-substrate:  0.916
CYP3A4-inhibitor:  0.042
CYP3A4-substrate:  0.722

ADMET: Excretion

Clearance (CL):  4.796
Half-life (T1/2):  0.049

ADMET: Toxicity

hERG Blockers:  0.953
Human Hepatotoxicity (H-HT):  0.97
Drug-inuced Liver Injury (DILI):  0.791
AMES Toxicity:  0.361
Rat Oral Acute Toxicity:  0.925
Maximum Recommended Daily Dose:  0.616
Skin Sensitization:  0.939
Carcinogencity:  0.439
Eye Corrosion:  0.004
Eye Irritation:  0.117
Respiratory Toxicity:  0.989

Download Data

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

  Natural Product: NPC84178

Natural Product ID:  NPC84178
Common Name*:   CEGDZSHEIZACBG-UHFFFAOYSA-L
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CEGDZSHEIZACBG-UHFFFAOYSA-L
Standard InCHI:  InChI=1S/C8H11N.H2O4S/c9-7-6-8-4-2-1-3-5-8;1-5(2,3)4/h1-5H,6-7,9H2;(H2,1,2,3,4)/p-2
SMILES:  c1ccc(cc1)CCN.[O-]S(=O)(=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6365704
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000186] Phenethylamines

*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
NPO24476.1 Phellodendron amurense var. wilsonii Varieties Rutaceae Eukaryota Leaves n.a. n.a. PMID[14510598]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30194 Crataegus spp Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24476.1 Phellodendron amurense var. wilsonii Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24476.1 Phellodendron amurense var. wilsonii Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30607 Coprinus atramentarius Species Agaricaceae 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]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24476 Phellodendron amurense Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15961 Sida cordifolia Species Malvaceae 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 NPC84178 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 NPC84178 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