Structure

Physi-Chem Properties

Molecular Weight:  306.26
Volume:  349.671
LogP:  4.588
LogD:  4.326
LogS:  -4.255
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.702
Synthetic Accessibility Score:  5.089
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.52
MDCK Permeability:  2.8215583370183595e-05
Pgp-inhibitor:  0.031
Pgp-substrate:  0.694
Human Intestinal Absorption (HIA):  0.776
20% Bioavailability (F20%):  0.54
30% Bioavailability (F30%):  0.609

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.723
Plasma Protein Binding (PPB):  92.36984252929688%
Volume Distribution (VD):  0.882
Pgp-substrate:  3.0361313819885254%

ADMET: Metabolism

CYP1A2-inhibitor:  0.078
CYP1A2-substrate:  0.499
CYP2C19-inhibitor:  0.142
CYP2C19-substrate:  0.761
CYP2C9-inhibitor:  0.274
CYP2C9-substrate:  0.82
CYP2D6-inhibitor:  0.126
CYP2D6-substrate:  0.378
CYP3A4-inhibitor:  0.486
CYP3A4-substrate:  0.29

ADMET: Excretion

Clearance (CL):  4.924
Half-life (T1/2):  0.323

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.161
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.053
Maximum Recommended Daily Dose:  0.963
Skin Sensitization:  0.894
Carcinogencity:  0.055
Eye Corrosion:  0.077
Eye Irritation:  0.464
Respiratory Toxicity:  0.311

Download Data

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

  Natural Product: NPC93431

Natural Product ID:  NPC93431
Common Name*:   OEJLZKSNBNTNEI-DAJYPMNESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OEJLZKSNBNTNEI-DAJYPMNESA-N
Standard InCHI:  InChI=1S/C20H34O2/c1-14-7-6-8-15(2)13-17(21)18-16(19(3,4)22)10-12-20(18,5)11-9-14/h8-9,11,14,16-18,21-22H,6-7,10,12-13H2,1-5H3/b11-9+,15-8+/t14-,16+,17-,18+,20-/m0/s1
SMILES:  C[C@H]1CC/C=C(C)/C[C@@H]([C@H]2[C@@H](CC[C@]2(C)/C=C/1)C(C)(C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001760] Dolabellane and neodolabellane diterpenoids

*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
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota roots n.a. n.a. PMID[11325249]
NPO6812 Bulbine frutescens Species Xanthorrhoeaceae Eukaryota n.a. root n.a. PMID[12193014]
NPO8948 Streptomyces pristinaespiralis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[25708513]
NPO8796 Cnemidocarpa bicornuta Species Styelidae Eukaryota n.a. New Zealand n.a. PMID[9644087]
NPO604 Erysimum crepidifolium Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO604 Erysimum crepidifolium Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9742 Entada scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19911 Arachniodes festina Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17330 Pseudopotamilla occelata Species Sabellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20488 Abies homolepis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO604 Erysimum crepidifolium Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26935 Coprinopsis lagopus Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20420 Helenium brevifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20558 Pseudevernia ericetorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8033 Sordaria macrospora Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6812 Bulbine frutescens Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20221 Maytenus truncata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7039 Espeletia uribei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5863 Amyris plumieri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1481 Balfourodendron riedelianum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12648 Uragoga ipecacuanha n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16389 Anodonta cygnea Species Unionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16565 Lindera oldhami Species Tineidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20838 Cleome pentaphylla Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12335 Aristolochia reticulata Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17838 Aster flaccidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21494 Eryngium maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8796 Cnemidocarpa bicornuta Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2958 Euphorbia glareosa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8948 Streptomyces pristinaespiralis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27967 Betula glandulosa Species Betulaceae 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 NPC93431 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 NPC93431 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