Structure

Physi-Chem Properties

Molecular Weight:  152.12
Volume:  170.557
LogP:  2.985
LogD:  3.21
LogS:  -2.036
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.569
Synthetic Accessibility Score:  4.435
Fsp3:  0.8
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:  -4.283
MDCK Permeability:  1.896542926260736e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.983
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.846
Plasma Protein Binding (PPB):  55.88567352294922%
Volume Distribution (VD):  1.101
Pgp-substrate:  47.826499938964844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.142
CYP1A2-substrate:  0.104
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.443
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.382
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.533
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.215

ADMET: Excretion

Clearance (CL):  8.859
Half-life (T1/2):  0.729

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.1
Drug-inuced Liver Injury (DILI):  0.668
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.971
Skin Sensitization:  0.646
Carcinogencity:  0.597
Eye Corrosion:  0.919
Eye Irritation:  0.991
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC216144

Natural Product ID:  NPC216144
Common Name*:   RXBQNMWIQKOSCS-BDAKNGLRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RXBQNMWIQKOSCS-BDAKNGLRSA-N
Standard InCHI:  InChI=1S/C10H16O/c1-10(2)8-4-3-7(6-11)9(10)5-8/h3,8-9,11H,4-6H2,1-2H3/t8-,9+/m1/s1
SMILES:  CC1(C)[C@@H]2CC=C(CO)[C@@H]1C2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6973635
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
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[10654416]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota roots n.a. n.a. PMID[12398547]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. seed n.a. PMID[14577694]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[18164718]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[20014777]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. seed n.a. PMID[21942765]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota seeds n.a. n.a. PMID[21942765]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[22459211]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[24195447]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota Gum resin n.a. n.a. PMID[26457560]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[28485933]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[547813]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12916 Radix et rhizoma rhodiolae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22230 Rhodiola crenulata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17333 Valeriana officinalis Species Caprifoliaceae 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 NPC216144 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 NPC216144 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