Structure

Physi-Chem Properties

Molecular Weight:  176.08
Volume:  194.654
LogP:  2.362
LogD:  2.051
LogS:  -2.129
# Rotatable Bonds:  4
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.66
Synthetic Accessibility Score:  1.855
Fsp3:  0.182
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:  -4.218
MDCK Permeability:  3.471566014923155e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.893

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.983
Plasma Protein Binding (PPB):  47.500240325927734%
Volume Distribution (VD):  1.639
Pgp-substrate:  37.784271240234375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.119
CYP2C19-inhibitor:  0.27
CYP2C19-substrate:  0.395
CYP2C9-inhibitor:  0.045
CYP2C9-substrate:  0.024
CYP2D6-inhibitor:  0.103
CYP2D6-substrate:  0.091
CYP3A4-inhibitor:  0.099
CYP3A4-substrate:  0.294

ADMET: Excretion

Clearance (CL):  8.342
Half-life (T1/2):  0.894

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.262
Drug-inuced Liver Injury (DILI):  0.831
AMES Toxicity:  0.592
Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.46
Carcinogencity:  0.566
Eye Corrosion:  0.279
Eye Irritation:  0.984
Respiratory Toxicity:  0.051

Download Data

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

  Natural Product: NPC25836

Natural Product ID:  NPC25836
Common Name*:   WJSDHUCWMSHDCR-YVMONPNESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WJSDHUCWMSHDCR-YVMONPNESA-N
Standard InCHI:  InChI=1S/C11H12O2/c1-10(12)13-9-5-8-11-6-3-2-4-7-11/h2-8H,9H2,1H3/b8-5-
SMILES:  CC(=O)OC/C=Cc1ccccc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315912
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000037] Styrenes

*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
NPO31458 Cinnamomum cassia Species Lauraceae Eukaryota twigs n.a. n.a. PMID[19555125]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. bark n.a. PMID[21875098]
NPO31458 Cinnamomum cassia Species Lauraceae Eukaryota twigs n.a. n.a. PMID[22677314]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[24868863]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25089845]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[28682072]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[29883114]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota Bark n.a. n.a. PMID[33151073]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31458 Cinnamomum cassia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1254 Cynanchum bungei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6892 Oleum corticis cinnamomi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO1254 Cynanchum bungei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1254 Cynanchum bungei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31458 Cinnamomum cassia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9546 Cinamomum cassia n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20093 Cupaniopsis trigonocarpa Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23140 Spongosorites ruetzleri Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19438 Alpinia nutans Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3689 Cinnamomum verum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22393 Piper lowong Species Piperaceae 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
NPO3689 NPC25836 Other Bark 127.5 51 204 mg/100g Database [DUKE]

☑ 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 NPC25836 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 NPC25836 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