Structure

Physi-Chem Properties

Molecular Weight:  208.07
Volume:  212.234
LogP:  1.063
LogD:  1.178
LogS:  -1.95
# Rotatable Bonds:  3
TPSA:  56.51
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.56
Synthetic Accessibility Score:  2.628
Fsp3:  0.273
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:  -4.572
MDCK Permeability:  2.050132206932176e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.129
Plasma Protein Binding (PPB):  79.22025299072266%
Volume Distribution (VD):  0.99
Pgp-substrate:  15.96833610534668%

ADMET: Metabolism

CYP1A2-inhibitor:  0.944
CYP1A2-substrate:  0.948
CYP2C19-inhibitor:  0.242
CYP2C19-substrate:  0.531
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.78
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.812
CYP3A4-inhibitor:  0.053
CYP3A4-substrate:  0.38

ADMET: Excretion

Clearance (CL):  10.791
Half-life (T1/2):  0.744

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.606
Drug-inuced Liver Injury (DILI):  0.42
AMES Toxicity:  0.412
Rat Oral Acute Toxicity:  0.88
Maximum Recommended Daily Dose:  0.215
Skin Sensitization:  0.631
Carcinogencity:  0.889
Eye Corrosion:  0.654
Eye Irritation:  0.984
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC32338

Natural Product ID:  NPC32338
Common Name*:   VVYCRPVWBIEKIW-SNAWJCMRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VVYCRPVWBIEKIW-SNAWJCMRSA-N
Standard InCHI:  InChI=1S/C11H12O4/c1-4-5-8(12)11-7(2)15-10(13)6-9(11)14-3/h4-6H,1-3H3/b5-4+
SMILES:  C/C=C/C(=O)c1c(C)oc(=O)cc1OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6312351
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones

*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
NPO8725 Aristolochia indica Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[6539809]
NPO8725 Aristolochia indica Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8725 Aristolochia indica Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8725 Aristolochia indica Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO847 Bignonia venusta Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11653 Sargassum ringoldianum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2751 Berchemia zeyheri Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10988 Crambe chelastra Species Esperiopsidae 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 9300.0 nM PMID[543197]
NPT81 Cell Line A549 Homo sapiens IC50 = 12900.0 nM PMID[543197]
NPT1229 Cell Line Huh-7 Homo sapiens IC50 = 8600.0 nM PMID[543197]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 2600.0 nM PMID[543197]
NPT165 Cell Line HeLa Homo sapiens Activity = 0.0 % PMID[543197]
NPT165 Cell Line HeLa Homo sapiens Activity = 2.0 % PMID[543197]
NPT165 Cell Line HeLa Homo sapiens Activity = 7.0 % PMID[543197]
NPT165 Cell Line HeLa Homo sapiens Activity = 14.0 % PMID[543197]

☑ 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 NPC32338 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 NPC32338 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