Structure

Physi-Chem Properties

Molecular Weight:  254.09
Volume:  267.538
LogP:  3.313
LogD:  3.171
LogS:  -4.836
# Rotatable Bonds:  2
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.824
Synthetic Accessibility Score:  2.382
Fsp3:  0.188
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.629
MDCK Permeability:  2.3207290723803453e-05
Pgp-inhibitor:  0.962
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.118

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.341
Plasma Protein Binding (PPB):  96.36491394042969%
Volume Distribution (VD):  0.484
Pgp-substrate:  2.3745720386505127%

ADMET: Metabolism

CYP1A2-inhibitor:  0.876
CYP1A2-substrate:  0.936
CYP2C19-inhibitor:  0.969
CYP2C19-substrate:  0.315
CYP2C9-inhibitor:  0.912
CYP2C9-substrate:  0.901
CYP2D6-inhibitor:  0.511
CYP2D6-substrate:  0.89
CYP3A4-inhibitor:  0.696
CYP3A4-substrate:  0.332

ADMET: Excretion

Clearance (CL):  9.071
Half-life (T1/2):  0.166

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.187
Drug-inuced Liver Injury (DILI):  0.888
AMES Toxicity:  0.822
Rat Oral Acute Toxicity:  0.359
Maximum Recommended Daily Dose:  0.409
Skin Sensitization:  0.123
Carcinogencity:  0.639
Eye Corrosion:  0.01
Eye Irritation:  0.88
Respiratory Toxicity:  0.662

Download Data

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

  Natural Product: NPC485642

Natural Product ID:  NPC485642
Common Name*:   VYESEQLQFXUROZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VYESEQLQFXUROZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H14O3/c1-18-12-7-8-13-14(17)10-15(19-16(13)9-12)11-5-3-2-4-6-11/h2-9,15H,10H2,1H3
SMILES:  COc1ccc2C(=O)CC(c3ccccc3)Oc2c1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   2825024
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26690274]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25653 Spatholobus suberectus Species Fabaceae 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
NPT441 Individual Protein Cytochrome P450 19A1 Homo sapiens IC50 = 8000.0 nM PMID[11909717]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 35700.0 nM PMID[11720850]
NPT441 Individual Protein Cytochrome P450 19A1 Homo sapiens IC50 = 8000.0 nM PMID[12270163]
NPT441 Individual Protein Cytochrome P450 19A1 Homo sapiens IC50 = 8000.0 nM PMID[18042388]
NPT441 Individual Protein Cytochrome P450 19A1 Homo sapiens Activity = 0.7 n.a. PMID[18042388]
NPT71 Cell Line HEK293 Homo sapiens FC = 1.1 n.a. PMID[19307119]
NPT582 Individual Protein Monoamine oxidase B Homo sapiens IC50 = 1470.0 nM PMID[20045650]
NPT1443 Individual Protein Pyruvate dehydrogenase kinase isoform 1 Homo sapiens Inhibition = 4.97 % PMID[28049590]
NPT2 Others Unspecified Ratio IC50 > 68.0 n.a. PMID[20045650]

☑ 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 NPC485642 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 NPC485642 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