Structure

Physi-Chem Properties

Molecular Weight:  168.12
Volume:  179.347
LogP:  2.552
LogD:  2.434
LogS:  -2.73
# Rotatable Bonds:  1
TPSA:  18.46
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.442
Synthetic Accessibility Score:  5.682
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.298
MDCK Permeability:  2.648391637194436e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.131
Plasma Protein Binding (PPB):  80.00188446044922%
Volume Distribution (VD):  1.556
Pgp-substrate:  27.859792709350586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.107
CYP1A2-substrate:  0.87
CYP2C19-inhibitor:  0.113
CYP2C19-substrate:  0.943
CYP2C9-inhibitor:  0.074
CYP2C9-substrate:  0.202
CYP2D6-inhibitor:  0.06
CYP2D6-substrate:  0.762
CYP3A4-inhibitor:  0.44
CYP3A4-substrate:  0.609

ADMET: Excretion

Clearance (CL):  5.372
Half-life (T1/2):  0.525

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.256
Drug-inuced Liver Injury (DILI):  0.114
AMES Toxicity:  0.152
Rat Oral Acute Toxicity:  0.073
Maximum Recommended Daily Dose:  0.037
Skin Sensitization:  0.561
Carcinogencity:  0.884
Eye Corrosion:  0.098
Eye Irritation:  0.955
Respiratory Toxicity:  0.283

Download Data

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

  Natural Product: NPC168518

Natural Product ID:  NPC168518
Common Name*:   Ascaridole
IUPAC Name:   1-methyl-4-propan-2-yl-2,3-dioxabicyclo[2.2.2]oct-5-ene
Synonyms:   Ascaridole
Standard InCHIKey:  MGYMHQJELJYRQS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H16O2/c1-8(2)10-6-4-9(3,5-7-10)11-12-10/h4,6,8H,5,7H2,1-3H3
SMILES:  CC(C12CCC(OO1)(C=C2)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL467614
PubChem CID:   10545
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000368] Dioxanes
        • [CHEMONTID:0001312] 1,2-dioxanes

*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
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[11975490]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. leaf n.a. PMID[15388977]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. stem n.a. PMID[17202689]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18679750]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. pericarp n.a. PMID[20628994]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[24175626]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7698 Elettaria cardamomum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9290 Zanthoxylum piperitum Species Rutaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC80 > 500.0 uM PMID[545687]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 500000.0 nM PMID[545687]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 74.8 % PMID[545687]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi MLC = 23.0 uM PMID[545688]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 8.5 % PMID[545688]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Activity = 22.8 n.a. PMID[545688]
NPT4910 Organism Aphelenchoides besseyi Aphelenchoides besseyi LC50 = 365.0 ug.mL-1 PMID[545689]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita LC50 = 52.0 ug.mL-1 PMID[545689]
NPT4910 Organism Aphelenchoides besseyi Aphelenchoides besseyi mortality < 50.0 % PMID[545689]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita mortality = 100.0 % PMID[545689]

☑ 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 NPC168518 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
1.0 High Similarity NPC105780
0.8148 Intermediate Similarity NPC294358
0.8148 Intermediate Similarity NPC40417
0.7143 Intermediate Similarity NPC174956
0.7097 Intermediate Similarity NPC66020
0.7042 Intermediate Similarity NPC474230
0.7042 Intermediate Similarity NPC475025
0.7031 Intermediate Similarity NPC300593
0.7018 Intermediate Similarity NPC214584
0.7018 Intermediate Similarity NPC26906
0.7015 Intermediate Similarity NPC474900
0.7 Intermediate Similarity NPC133580
0.6984 Remote Similarity NPC68679
0.6984 Remote Similarity NPC207007
0.6984 Remote Similarity NPC321867
0.6957 Remote Similarity NPC259049
0.6901 Remote Similarity NPC474231
0.6897 Remote Similarity NPC157781
0.6897 Remote Similarity NPC179169
0.6897 Remote Similarity NPC181255
0.6897 Remote Similarity NPC35519
0.6897 Remote Similarity NPC68014
0.6897 Remote Similarity NPC306195
0.6842 Remote Similarity NPC329773
0.6818 Remote Similarity NPC267027
0.6806 Remote Similarity NPC475027
0.6721 Remote Similarity NPC141699
0.6721 Remote Similarity NPC274396
0.6716 Remote Similarity NPC73603
0.6667 Remote Similarity NPC15162
0.6667 Remote Similarity NPC475931
0.6618 Remote Similarity NPC471238
0.6615 Remote Similarity NPC81615
0.6613 Remote Similarity NPC165808
0.661 Remote Similarity NPC177112
0.661 Remote Similarity NPC71506
0.6571 Remote Similarity NPC23954
0.6571 Remote Similarity NPC471272
0.6567 Remote Similarity NPC279434
0.6562 Remote Similarity NPC240506
0.6562 Remote Similarity NPC99487
0.6552 Remote Similarity NPC131623
0.6522 Remote Similarity NPC74722
0.6522 Remote Similarity NPC471560
0.6522 Remote Similarity NPC304690
0.6508 Remote Similarity NPC155025
0.6508 Remote Similarity NPC181872
0.6479 Remote Similarity NPC130665
0.6462 Remote Similarity NPC194208
0.6462 Remote Similarity NPC63111
0.6462 Remote Similarity NPC282694
0.6462 Remote Similarity NPC79576
0.6452 Remote Similarity NPC179024
0.6418 Remote Similarity NPC471200
0.6349 Remote Similarity NPC278550
0.6324 Remote Similarity NPC230107
0.6324 Remote Similarity NPC202017
0.6308 Remote Similarity NPC323153
0.6308 Remote Similarity NPC135648
0.6301 Remote Similarity NPC85831
0.6301 Remote Similarity NPC215215
0.6301 Remote Similarity NPC265921
0.629 Remote Similarity NPC148163
0.629 Remote Similarity NPC148216
0.629 Remote Similarity NPC227135
0.629 Remote Similarity NPC130209
0.6286 Remote Similarity NPC473893
0.625 Remote Similarity NPC265485
0.625 Remote Similarity NPC220939
0.625 Remote Similarity NPC226848
0.6232 Remote Similarity NPC474477
0.6232 Remote Similarity NPC68703
0.6232 Remote Similarity NPC69649
0.6232 Remote Similarity NPC136813
0.623 Remote Similarity NPC192962
0.6216 Remote Similarity NPC474447
0.6216 Remote Similarity NPC268111
0.6212 Remote Similarity NPC225342
0.6212 Remote Similarity NPC41160
0.6212 Remote Similarity NPC210346
0.6212 Remote Similarity NPC469728
0.6197 Remote Similarity NPC472017
0.6197 Remote Similarity NPC34834
0.619 Remote Similarity NPC39068
0.6184 Remote Similarity NPC204270
0.6184 Remote Similarity NPC233295
0.6176 Remote Similarity NPC205618
0.6176 Remote Similarity NPC469326
0.6176 Remote Similarity NPC261782
0.6176 Remote Similarity NPC308844
0.6173 Remote Similarity NPC304083
0.6167 Remote Similarity NPC251335
0.6164 Remote Similarity NPC330016
0.6164 Remote Similarity NPC201048
0.6164 Remote Similarity NPC476366
0.6154 Remote Similarity NPC143810
0.6154 Remote Similarity NPC279186
0.6154 Remote Similarity NPC122239
0.6154 Remote Similarity NPC5698
0.6154 Remote Similarity NPC83838
0.6143 Remote Similarity NPC96484
0.6133 Remote Similarity NPC281296
0.6133 Remote Similarity NPC149550
0.6133 Remote Similarity NPC85105
0.6119 Remote Similarity NPC473508
0.6111 Remote Similarity NPC126061
0.6111 Remote Similarity NPC164022
0.6111 Remote Similarity NPC471268
0.6111 Remote Similarity NPC471660
0.6111 Remote Similarity NPC471271
0.6104 Remote Similarity NPC233332
0.6104 Remote Similarity NPC186072
0.6098 Remote Similarity NPC475605
0.6098 Remote Similarity NPC212596
0.6098 Remote Similarity NPC4574
0.6087 Remote Similarity NPC476406
0.6087 Remote Similarity NPC116013
0.6087 Remote Similarity NPC311736
0.6087 Remote Similarity NPC327815
0.6087 Remote Similarity NPC42630
0.6087 Remote Similarity NPC326310
0.6081 Remote Similarity NPC32832
0.6076 Remote Similarity NPC44261
0.6066 Remote Similarity NPC208638
0.6061 Remote Similarity NPC127824
0.6061 Remote Similarity NPC176621
0.6056 Remote Similarity NPC107130
0.6056 Remote Similarity NPC265574
0.6056 Remote Similarity NPC329989
0.6056 Remote Similarity NPC476431
0.6056 Remote Similarity NPC239373
0.6056 Remote Similarity NPC474248
0.6053 Remote Similarity NPC477089
0.6053 Remote Similarity NPC121200
0.6053 Remote Similarity NPC470944
0.6049 Remote Similarity NPC470415
0.6032 Remote Similarity NPC251666
0.6032 Remote Similarity NPC223604
0.6032 Remote Similarity NPC218525
0.6032 Remote Similarity NPC232247
0.6029 Remote Similarity NPC107540
0.6027 Remote Similarity NPC474543
0.6027 Remote Similarity NPC167145
0.6027 Remote Similarity NPC238425
0.6027 Remote Similarity NPC68443
0.6027 Remote Similarity NPC472018
0.6026 Remote Similarity NPC15978
0.6026 Remote Similarity NPC226068
0.6026 Remote Similarity NPC47761
0.6024 Remote Similarity NPC101886
0.6 Remote Similarity NPC171225
0.6 Remote Similarity NPC88454
0.6 Remote Similarity NPC469514
0.6 Remote Similarity NPC163290
0.6 Remote Similarity NPC470749
0.6 Remote Similarity NPC265588
0.6 Remote Similarity NPC10017
0.6 Remote Similarity NPC82337
0.6 Remote Similarity NPC472305
0.6 Remote Similarity NPC101307
0.6 Remote Similarity NPC477791
0.6 Remote Similarity NPC152017
0.6 Remote Similarity NPC188596
0.6 Remote Similarity NPC144023
0.6 Remote Similarity NPC253190
0.6 Remote Similarity NPC117607
0.6 Remote Similarity NPC278895
0.5974 Remote Similarity NPC469617
0.5972 Remote Similarity NPC475728
0.5972 Remote Similarity NPC92801
0.5972 Remote Similarity NPC69462
0.597 Remote Similarity NPC475251
0.5968 Remote Similarity NPC165755
0.5952 Remote Similarity NPC14380
0.5946 Remote Similarity NPC306727
0.5946 Remote Similarity NPC22134
0.5946 Remote Similarity NPC474551
0.5946 Remote Similarity NPC190859
0.5942 Remote Similarity NPC61503
0.5942 Remote Similarity NPC19569
0.5938 Remote Similarity NPC48891
0.5938 Remote Similarity NPC264779
0.5932 Remote Similarity NPC100445
0.5921 Remote Similarity NPC476439
0.5921 Remote Similarity NPC470758
0.5921 Remote Similarity NPC34110
0.5921 Remote Similarity NPC132542
0.5921 Remote Similarity NPC470711
0.5921 Remote Similarity NPC470750
0.5921 Remote Similarity NPC107668
0.5921 Remote Similarity NPC91594
0.5915 Remote Similarity NPC94192
0.5915 Remote Similarity NPC272961
0.5915 Remote Similarity NPC224532
0.5915 Remote Similarity NPC139785
0.5915 Remote Similarity NPC476945
0.5915 Remote Similarity NPC167527
0.5915 Remote Similarity NPC117804
0.5909 Remote Similarity NPC469321
0.5904 Remote Similarity NPC475101

  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 NPC168518 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
0.6984 Remote Similarity NPD368 Approved
0.629 Remote Similarity NPD342 Phase 1
0.5867 Remote Similarity NPD8264 Approved
0.5844 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5789 Remote Similarity NPD367 Approved
0.5733 Remote Similarity NPD6926 Approved
0.5733 Remote Similarity NPD4785 Approved
0.5733 Remote Similarity NPD6924 Approved
0.5733 Remote Similarity NPD4784 Approved
0.5714 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5696 Remote Similarity NPD7332 Phase 2
0.5696 Remote Similarity NPD7514 Phase 3
0.5676 Remote Similarity NPD4243 Approved

  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