Structure

Physi-Chem Properties

Molecular Weight:  208.15
Volume:  234.519
LogP:  2.113
LogD:  1.602
LogS:  -2.161
# Rotatable Bonds:  2
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.654
Synthetic Accessibility Score:  3.772
Fsp3:  0.692
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:  -4.538
MDCK Permeability:  2.5380601073266007e-05
Pgp-inhibitor:  0.09
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.961
Plasma Protein Binding (PPB):  90.42562103271484%
Volume Distribution (VD):  0.872
Pgp-substrate:  13.417484283447266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.031
CYP1A2-substrate:  0.154
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.864
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.193
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.386
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.434

ADMET: Excretion

Clearance (CL):  8.361
Half-life (T1/2):  0.711

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.222
Drug-inuced Liver Injury (DILI):  0.247
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.33
Maximum Recommended Daily Dose:  0.881
Skin Sensitization:  0.408
Carcinogencity:  0.903
Eye Corrosion:  0.255
Eye Irritation:  0.557
Respiratory Toxicity:  0.816

Download Data

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

  Natural Product: NPC176345

Natural Product ID:  NPC176345
Common Name*:   LWWWERIIOIAWQK-VUHVRTRXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LWWWERIIOIAWQK-VUHVRTRXSA-N
Standard InCHI:  InChI=1S/C13H20O2/c1-9(14)5-6-11-10(2)12(15)7-8-13(11,3)4/h5-6,9,14H,7-8H2,1-4H3/b6-5+/t9-/m1/s1
SMILES:  C[C@H](/C=C/C1=C(C)C(=O)CCC1(C)C)O
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:0001550] Sesquiterpenoids

*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
NPO28152 Jacaranda caucana Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[19361168]
NPO11450 Pseudoceratina purpurea Species Pseudoceratinidae Eukaryota n.a. n.a. n.a. PMID[26035239]
NPO11450 Pseudoceratina purpurea Species Pseudoceratinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26838 Adenophora triphylla Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29214 Teucrium massiliense Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26838 Adenophora triphylla Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28095 Boronia megastigma Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15808 Vibrio gazogenes Species Vibrionaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27879 Ailanthus triphysa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20978 Alternaria cinerariae Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28117 Tor sinensis Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27588 Carpolobia lutea Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23311 Libanothamnus tamanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8266 Solanum anguivi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27219 Gonioma kamassi Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27948 Licania carii Species Chrysobalanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28152 Jacaranda caucana Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27381 Hypselodoris webbi Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27985 Plantago arenaria Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11450 Pseudoceratina purpurea Species Pseudoceratinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1650 Boykinia watanabei Species Saxifragaceae 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 NPC176345 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 NPC176345 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