Structure

Physi-Chem Properties

Molecular Weight:  297.16
Volume:  297.922
LogP:  0.687
LogD:  -0.018
LogS:  -1.873
# Rotatable Bonds:  5
TPSA:  91.18
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.594
Synthetic Accessibility Score:  3.394
Fsp3:  0.6
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:  -5.748
MDCK Permeability:  1.0109867616847623e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.426
Human Intestinal Absorption (HIA):  0.387
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.42

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.299
Plasma Protein Binding (PPB):  47.586875915527344%
Volume Distribution (VD):  1.426
Pgp-substrate:  51.3924674987793%

ADMET: Metabolism

CYP1A2-inhibitor:  0.115
CYP1A2-substrate:  0.322
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.876
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.423
CYP2D6-inhibitor:  0.095
CYP2D6-substrate:  0.768
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.153

ADMET: Excretion

Clearance (CL):  4.019
Half-life (T1/2):  0.548

ADMET: Toxicity

hERG Blockers:  0.61
Human Hepatotoxicity (H-HT):  0.442
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.281
Rat Oral Acute Toxicity:  0.623
Maximum Recommended Daily Dose:  0.388
Skin Sensitization:  0.775
Carcinogencity:  0.035
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.915

Download Data

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

  Natural Product: NPC121051

Natural Product ID:  NPC121051
Common Name*:   QHOKXDBQIFVQBR-QJPTWQEYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QHOKXDBQIFVQBR-QJPTWQEYSA-N
Standard InCHI:  InChI=1S/C12H16O2/c1-8-3-4-11(14)12(2)6-5-9(13)7-10(8)12/h5-6,10-11,14H,1,3-4,7H2,2H3/t10-,11+,12+/m0/s1
SMILES:  C=C1CC[C@H]([C@]2(C)C=CC(=O)C[C@@H]12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11148221
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

*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
NPO25111 Streptomyces tanashiensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)84249-0]
NPO24121 Vernoniopsis caudata n.a. n.a. n.a. n.a. n.a. n.a. PMID[15921436]
NPO20815 Lindera fruticosa Species Lauraceae Eukaryota roots n.a. n.a. PMID[16724860]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[26509914]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22713 Aquilegia flabellata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23948 Serratia plymuthica Species Yersiniaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20936 Arecastrum romanzoffianum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23676 Fleroya rubrostipulata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21683 Selaginella lepidophylla Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20815 Lindera fruticosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18589 Allopora californica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16184 Asclepias asperula Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14448 Laurencia venusta Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24776 Euryops jacksonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23843 Clerodendrum grayi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21121 Ips japonicus Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16971 Sparassis crispa Species Sparassidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23445 Vernonia triflosculosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23158 Penicillium carminoviolaceum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13388 Lithophyllum incrustans Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24121 Vernoniopsis caudata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23376 Genista aetnensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17668 Artemisia gmelinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25111 Streptomyces tanashiensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24411 Pentaspadon motleyi Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20226 Artemisia filatovae 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 NPC121051 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 NPC121051 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