Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  263.658
LogP:  2.383
LogD:  2.804
LogS:  -3.425
# 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:  -4.851
MDCK Permeability:  4.6150555135682225e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.028
30% Bioavailability (F30%):  0.858

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.202
Plasma Protein Binding (PPB):  73.39614868164062%
Volume Distribution (VD):  1.144
Pgp-substrate:  27.79102897644043%

ADMET: Metabolism

CYP1A2-inhibitor:  0.246
CYP1A2-substrate:  0.171
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.73
CYP2C9-inhibitor:  0.065
CYP2C9-substrate:  0.081
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.301
CYP3A4-inhibitor:  0.094
CYP3A4-substrate:  0.294

ADMET: Excretion

Clearance (CL):  8.31
Half-life (T1/2):  0.608

ADMET: Toxicity

hERG Blockers:  0.07
Human Hepatotoxicity (H-HT):  0.734
Drug-inuced Liver Injury (DILI):  0.831
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.795
Maximum Recommended Daily Dose:  0.122
Skin Sensitization:  0.598
Carcinogencity:  0.39
Eye Corrosion:  0.667
Eye Irritation:  0.632
Respiratory Toxicity:  0.97

Download Data

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

  Natural Product: NPC277806

Natural Product ID:  NPC277806
Common Name*:   XPNBRTWIMIGGMT-MIPSWGQUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XPNBRTWIMIGGMT-MIPSWGQUSA-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:   100302
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
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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]
NPO18577 Lathyrus roseus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16848 Nasutitermes nigriceps Species Termitoidae 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]
NPO15114 Oxalis pes-caprae Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18919 Helenium amarum Species Asteraceae 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]

☑ 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 NPC277806 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 NPC277806 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