Structure

Physi-Chem Properties

Molecular Weight:  368.13
Volume:  381.036
LogP:  2.742
LogD:  2.82
LogS:  -3.921
# Rotatable Bonds:  8
TPSA:  93.06
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.548
Synthetic Accessibility Score:  2.426
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.834
MDCK Permeability:  1.632656858419068e-05
Pgp-inhibitor:  0.284
Pgp-substrate:  0.014
Human Intestinal Absorption (HIA):  0.06
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.171

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.103
Plasma Protein Binding (PPB):  99.7994613647461%
Volume Distribution (VD):  0.369
Pgp-substrate:  1.0492939949035645%

ADMET: Metabolism

CYP1A2-inhibitor:  0.593
CYP1A2-substrate:  0.758
CYP2C19-inhibitor:  0.287
CYP2C19-substrate:  0.12
CYP2C9-inhibitor:  0.661
CYP2C9-substrate:  0.906
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.895
CYP3A4-inhibitor:  0.674
CYP3A4-substrate:  0.517

ADMET: Excretion

Clearance (CL):  13.839
Half-life (T1/2):  0.948

ADMET: Toxicity

hERG Blockers:  0.214
Human Hepatotoxicity (H-HT):  0.475
Drug-inuced Liver Injury (DILI):  0.895
AMES Toxicity:  0.234
Rat Oral Acute Toxicity:  0.896
Maximum Recommended Daily Dose:  0.776
Skin Sensitization:  0.958
Carcinogencity:  0.706
Eye Corrosion:  0.007
Eye Irritation:  0.792
Respiratory Toxicity:  0.951

Download Data

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

  Natural Product: NPC224020

Natural Product ID:  NPC224020
Common Name*:   TWORTZAXDSRCIT-ZKCHVHJHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  TWORTZAXDSRCIT-ZKCHVHJHSA-N
Standard InCHI:  InChI=1S/C8H16O3/c9-6-5-8(11)3-1-7(10)2-4-8/h7,9-11H,1-6H2/t7-,8-
SMILES:  C1C[C@](CC[C@H]1O)(CCO)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:0001661] Secondary alcohols
            • [CHEMONTID:0002647] Cyclohexanols

*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
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. PMID[11429991]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17191679]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14110 Marrubium peregrinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5445 Euonymus nanus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11013 Tephrosia polyphylla Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15660 Afzelia bella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23838 Kitasatospora kifunensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6987 Tolypothrix byssoidea Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4214 Centaurea collina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11437 Alluaudia ascendens Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8231 Jaspis digonoxea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10196 Echinocereus blanckii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14110 Marrubium peregrinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4489 Achillea serbica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11189 Anabaena sphaerica Species 0stocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8719 Fusarium vasinfectum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10826 Rabdosia weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17430 Acacia retinoide Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO228 Physostigma venenosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6710 Sinapis nigra Species Brassicaceae 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 NPC224020 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 NPC224020 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