Structure

Physi-Chem Properties

Molecular Weight:  200.1
Volume:  202.848
LogP:  0.444
LogD:  0.858
LogS:  -1.306
# Rotatable Bonds:  0
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.438
Synthetic Accessibility Score:  4.356
Fsp3:  0.7
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:  -4.834
MDCK Permeability:  0.00013625821156892926
Pgp-inhibitor:  0.001
Pgp-substrate:  0.922
Human Intestinal Absorption (HIA):  0.026
20% Bioavailability (F20%):  0.911
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.655
Plasma Protein Binding (PPB):  63.454811096191406%
Volume Distribution (VD):  1.154
Pgp-substrate:  45.46807098388672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.042
CYP1A2-substrate:  0.104
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.6
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.761
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.413
CYP3A4-inhibitor:  0.025
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  7.197
Half-life (T1/2):  0.866

ADMET: Toxicity

hERG Blockers:  0.034
Human Hepatotoxicity (H-HT):  0.267
Drug-inuced Liver Injury (DILI):  0.194
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.287
Maximum Recommended Daily Dose:  0.989
Skin Sensitization:  0.509
Carcinogencity:  0.863
Eye Corrosion:  0.016
Eye Irritation:  0.358
Respiratory Toxicity:  0.602

Download Data

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

  Natural Product: NPC274388

Natural Product ID:  NPC274388
Common Name*:   DKWZZACTRIWLJJ-BKTAMIDGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DKWZZACTRIWLJJ-BKTAMIDGSA-N
Standard InCHI:  InChI=1S/C10H16O4/c1-7-6-9(12)3-2-8(11)4-5-10(13)14-7/h2-3,7-9,11-12H,4-6H2,1H3/b3-2+/t7-,8-,9-/m1/s1
SMILES:  C[C@@H]1C[C@@H](/C=C/[C@H](CCC(=O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24770096
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001796] Oxocins

*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
NPO33443 Stagonospora cirsii Species Massarinaceae Eukaryota n.a. n.a. n.a. PMID[18088096]
NPO33443 Stagonospora cirsii Species Massarinaceae Eukaryota n.a. n.a. n.a. PMID[18959441]
NPO1528 Dalea elegans Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21561780]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. fruit n.a. PMID[22396124]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8685 Hymenocallis arenicola Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4471 Blumea densiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO480 Hygrophila erecta Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24513 Streptomyces cyaneofuscatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9525 Relicina samoensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO743 Wardomyces inflatus Species Microascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6024 Cratoxylum formosum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8685 Hymenocallis arenicola Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1785 Corallina rubens Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1528 Dalea elegans 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

☑ 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 NPC274388 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 NPC274388 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