Structure

Physi-Chem Properties

Molecular Weight:  306.03
Volume:  228.728
LogP:  -0.044
LogD:  1.053
LogS:  0.767
# Rotatable Bonds:  3
TPSA:  20.23
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.671
Synthetic Accessibility Score:  2.669
Fsp3:  0.455
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:  -5.408
MDCK Permeability:  1.4574359738617204e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.649
Human Intestinal Absorption (HIA):  0.948
20% Bioavailability (F20%):  0.926
30% Bioavailability (F30%):  0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.254
Plasma Protein Binding (PPB):  19.964740753173828%
Volume Distribution (VD):  1.245
Pgp-substrate:  76.06183624267578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.919
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.506
CYP2D6-inhibitor:  0.099
CYP2D6-substrate:  0.932
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.149

ADMET: Excretion

Clearance (CL):  6.722
Half-life (T1/2):  0.952

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.216
Drug-inuced Liver Injury (DILI):  0.005
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.295
Maximum Recommended Daily Dose:  0.893
Skin Sensitization:  0.073
Carcinogencity:  0.035
Eye Corrosion:  0.04
Eye Irritation:  0.053
Respiratory Toxicity:  0.826

Download Data

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

  Natural Product: NPC21601

Natural Product ID:  NPC21601
Common Name*:   AFGLVJBHCHBOML-KHFPWOERSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AFGLVJBHCHBOML-KHFPWOERSA-N
Standard InCHI:  InChI=1S/C10H14O5/c1-4-7(11)2-5-6(9(12)13)3-15-10(14)8(4)5/h3-5,7-8,10-11,14H,2H2,1H3,(H,12,13)/t4-,5+,7-,8+,10+/m0/s1
SMILES:  C[C@H]1[C@H](C[C@@H]2C(=CO[C@H]([C@H]12)O)C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25026155
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001565] Iridoids and derivatives

*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
NPO22355 Flacourtia indica Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[23354072]
NPO26277 Euphorbia hirta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[32141299]
NPO26277 Euphorbia hirta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26277 Euphorbia hirta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16539 Viguiera puruana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26277 Euphorbia hirta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9983.1 Ambrosia artemisiifolia var. elatior Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6543 Parachlorella kessleri Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16539 Viguiera puruana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10470 Pimpinella major Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19646 Cynthia papillosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10942 Retama sphaerocarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14921 Anisothrix integra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26277 Euphorbia hirta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22355 Flacourtia indica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22459 Impatiens capensis Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16965 Lyngbya aestuarii Species Oscillatoriaceae Bacteria 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 NPC21601 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 NPC21601 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