Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  263.658
LogP:  2.155
LogD:  2.59
LogS:  -2.966
# Rotatable Bonds:  0
TPSA:  59.06
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.407
Synthetic Accessibility Score:  5.037
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.812
MDCK Permeability:  3.971501064370386e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.025
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.702

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.164
Plasma Protein Binding (PPB):  83.09593963623047%
Volume Distribution (VD):  1.158
Pgp-substrate:  16.43140411376953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.191
CYP1A2-substrate:  0.12
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.682
CYP2C9-inhibitor:  0.078
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.248
CYP3A4-inhibitor:  0.088
CYP3A4-substrate:  0.314

ADMET: Excretion

Clearance (CL):  7.506
Half-life (T1/2):  0.609

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.793
Drug-inuced Liver Injury (DILI):  0.913
AMES Toxicity:  0.036
Rat Oral Acute Toxicity:  0.653
Maximum Recommended Daily Dose:  0.046
Skin Sensitization:  0.634
Carcinogencity:  0.316
Eye Corrosion:  0.597
Eye Irritation:  0.768
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC23876

Natural Product ID:  NPC23876
Common Name*:   XPNBRTWIMIGGMT-DBWIBMCBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XPNBRTWIMIGGMT-DBWIBMCBSA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-6-4-9-8(7(2)14(17)18-9)5-15(3)10(6)11-12(19-11)13(15)16/h6,8-13,16H,2,4-5H2,1,3H3/t6-,8-,9+,10-,11-,12-,13+,15-/m1/s1
SMILES:  C[C@@H]1C[C@H]2[C@H](C[C@]3(C)[C@H]1[C@@H]1[C@H]([C@@H]3O)O1)C(=C)C(=O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones

*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
NPO15114 Oxalis pes-caprae Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9681 Toxicodendron diversilobum Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17502 Senecio jacquemontianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21499 Halimeda tuna Species Halimedaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8509 Senecio discolor Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16482 Hypoestes forskalei Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10732 Erysimum allionii Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28309 Artocarpus nitidus Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11615 Kopsia deverrei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17192 Licaria macrophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16848 Nasutitermes nigriceps Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18577 Lathyrus roseus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18249 Eucalyptus deglupta Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19131 Callilepis salicifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15631 Baccharis neaei Species Asteraceae 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 NPC23876 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 NPC23876 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