Structure

Physi-Chem Properties

Molecular Weight:  180.15
Volume:  205.149
LogP:  3.223
LogD:  2.869
LogS:  -2.884
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.568
Synthetic Accessibility Score:  3.78
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.482
MDCK Permeability:  2.481053707015235e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.307
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.396
Plasma Protein Binding (PPB):  71.5323715209961%
Volume Distribution (VD):  0.87
Pgp-substrate:  30.11212730407715%

ADMET: Metabolism

CYP1A2-inhibitor:  0.365
CYP1A2-substrate:  0.532
CYP2C19-inhibitor:  0.152
CYP2C19-substrate:  0.833
CYP2C9-inhibitor:  0.104
CYP2C9-substrate:  0.388
CYP2D6-inhibitor:  0.041
CYP2D6-substrate:  0.502
CYP3A4-inhibitor:  0.225
CYP3A4-substrate:  0.338

ADMET: Excretion

Clearance (CL):  8.833
Half-life (T1/2):  0.528

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.29
Drug-inuced Liver Injury (DILI):  0.205
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.236
Skin Sensitization:  0.422
Carcinogencity:  0.423
Eye Corrosion:  0.891
Eye Irritation:  0.976
Respiratory Toxicity:  0.273

Download Data

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

  Natural Product: NPC2098

Natural Product ID:  NPC2098
Common Name*:   ZBACDSGBJUIJGT-TUAOUCFPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZBACDSGBJUIJGT-TUAOUCFPSA-N
Standard InCHI:  InChI=1S/C12H20O/c1-9-5-3-4-6-11-10(9)7-8-12(11,2)13/h10-11,13H,1,3-8H2,2H3/t10-,11+,12-/m0/s1
SMILES:  C=C1CCCC[C@@H]2[C@H]1CC[C@]2(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota Root barks n.a. n.a. PMID[11473427]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota root bark n.a. n.a. PMID[18198838]
NPO7171 Salvia polystachya Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29135252]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7171 Salvia polystachya Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10830 Dictamnus dasycarpus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3560 Trifolium montanum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5799 Streptomyces chryseus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1329 Esenbeckia hartmanii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5451 Ageratina saltillensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11119 Salta triflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7171 Salvia polystachya Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7966 Grewia villosa Species Malvaceae 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 NPC2098 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 NPC2098 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