Structure

Physi-Chem Properties

Molecular Weight:  152.12
Volume:  170.557
LogP:  2.687
LogD:  2.79
LogS:  -3.289
# Rotatable Bonds:  1
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.563
Synthetic Accessibility Score:  4.208
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.395
MDCK Permeability:  2.939988553407602e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.173
30% Bioavailability (F30%):  0.498

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.963
Plasma Protein Binding (PPB):  75.16263580322266%
Volume Distribution (VD):  1.044
Pgp-substrate:  23.916263580322266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.524
CYP1A2-substrate:  0.575
CYP2C19-inhibitor:  0.136
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.066
CYP2C9-substrate:  0.179
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.393
CYP3A4-inhibitor:  0.209
CYP3A4-substrate:  0.354

ADMET: Excretion

Clearance (CL):  9.42
Half-life (T1/2):  0.72

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.261
Drug-inuced Liver Injury (DILI):  0.632
AMES Toxicity:  0.042
Rat Oral Acute Toxicity:  0.189
Maximum Recommended Daily Dose:  0.043
Skin Sensitization:  0.275
Carcinogencity:  0.361
Eye Corrosion:  0.951
Eye Irritation:  0.99
Respiratory Toxicity:  0.316

Download Data

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

  Natural Product: NPC233121

Natural Product ID:  NPC233121
Common Name*:   USMNOWBWPHYOEA-KHQFGBGNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  USMNOWBWPHYOEA-KHQFGBGNSA-N
Standard InCHI:  InChI=1S/C10H16O/c1-6(2)10-4-8(10)7(3)9(11)5-10/h6-8H,4-5H2,1-3H3/t7-,8+,10-/m1/s1
SMILES:  CC(C)[C@@]12C[C@H]2[C@@H](C)C(=O)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6553876
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001564] Bicyclic monoterpenoids

*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
NPO17534 Uvaria chamae Species Annonaceae Eukaryota roots n.a. n.a. PMID[15217292]
NPO17043 Lycopodium casuarinoides Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[18485717]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. PMID[19795841]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. PMID[4040154]
NPO17043 Lycopodium casuarinoides Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[7931368]
NPO17534 Uvaria chamae Species Annonaceae Eukaryota n.a. root n.a. PMID[845713]
NPO18720 Bertholletia excelsa Species Lecythidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO18720 Bertholletia excelsa Species Lecythidaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18720 Bertholletia excelsa Species Lecythidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17534 Uvaria chamae Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18720 Bertholletia excelsa Species Lecythidaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17534 Uvaria chamae Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17043 Lycopodium casuarinoides Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12942 Amphimedon terpenensis Species Niphatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18691 Mycale cecilia Species Mycalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15102 Senegalia tenuifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18465 Cryptocarya triplinervis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19944 Trichilia roka Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17043 Lycopodium casuarinoides Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20305 Stachytarpheta mutabilis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16185 Astilbe odontophylla Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19402 Salvadora oleoides Species Salvadoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21316.1 Barbarea vulgaris subsp. arcuata Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12304 Ascocoryne sarcoides Species Helotiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19654 Hydnocarpus venenata Species Achariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18199 Thermotoga maritima Species Thermotogaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18720 Bertholletia excelsa Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28689 Armillaria mellea Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5453.1 Euphorbia officinarum subsp. echinus Subspecies Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20948 Gynoxys buxifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19264 Macleaya cordata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18952 Sambucus nigra Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17534 Uvaria chamae Species Annonaceae 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 NPC233121 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 NPC233121 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