Structure

Physi-Chem Properties

Molecular Weight:  166.1
Volume:  176.711
LogP:  2.081
LogD:  1.736
LogS:  -2.904
# Rotatable Bonds:  0
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.512
Synthetic Accessibility Score:  4.122
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:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.603
MDCK Permeability:  2.5191204258590005e-05
Pgp-inhibitor:  0.032
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.091
Plasma Protein Binding (PPB):  84.21852111816406%
Volume Distribution (VD):  0.401
Pgp-substrate:  18.98301887512207%

ADMET: Metabolism

CYP1A2-inhibitor:  0.057
CYP1A2-substrate:  0.689
CYP2C19-inhibitor:  0.316
CYP2C19-substrate:  0.9
CYP2C9-inhibitor:  0.1
CYP2C9-substrate:  0.678
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.625
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.33

ADMET: Excretion

Clearance (CL):  4.377
Half-life (T1/2):  0.222

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.131
Drug-inuced Liver Injury (DILI):  0.09
AMES Toxicity:  0.158
Rat Oral Acute Toxicity:  0.256
Maximum Recommended Daily Dose:  0.187
Skin Sensitization:  0.171
Carcinogencity:  0.315
Eye Corrosion:  0.353
Eye Irritation:  0.91
Respiratory Toxicity:  0.871

Download Data

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

  Natural Product: NPC20017

Natural Product ID:  NPC20017
Common Name*:   4,7,7-Trimethylbicyclo[2.2.1]Heptane-2,3-Dione
IUPAC Name:   4,7,7-trimethylbicyclo[2.2.1]heptane-2,3-dione
Synonyms:  
Standard InCHIKey:  VNQXSTWCDUXYEZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H14O2/c1-9(2)6-4-5-10(9,3)8(12)7(6)11/h6H,4-5H2,1-3H3
SMILES:  O=C1C(=O)C2(C(C1CC2)(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL301431
PubChem CID:   25208
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
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. stem n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. flower n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. leaf n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. PMID[6387056]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26589 Artemisia annua L. Strain Asteraceae 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
NPT589 Individual Protein Serum albumin Bos taurus Log 1/C = 3.17 n.a. PMID[497833]
NPT27 Others Unspecified Log k' w = 1.225 n.a. PMID[497833]
NPT35 Others n.a. LogP = 1.52 n.a. PMID[497833]
NPT2 Others Unspecified Potency n.a. 1757.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 55092.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27611.8 nM PubChem BioAssay data set

☑ 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 NPC20017 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
0.9333 High Similarity NPC131981
0.9333 High Similarity NPC40249
0.9333 High Similarity NPC173996
0.8936 High Similarity NPC247786
0.8936 High Similarity NPC258672
0.8936 High Similarity NPC293343
0.8723 High Similarity NPC294440
0.8571 High Similarity NPC274182
0.8511 High Similarity NPC285814
0.8511 High Similarity NPC98246
0.8511 High Similarity NPC83187
0.766 Intermediate Similarity NPC18397
0.7556 Intermediate Similarity NPC223315
0.7455 Intermediate Similarity NPC143597
0.7455 Intermediate Similarity NPC151464
0.7407 Intermediate Similarity NPC53245
0.7407 Intermediate Similarity NPC288296
0.7391 Intermediate Similarity NPC141634
0.7273 Intermediate Similarity NPC184819
0.7241 Intermediate Similarity NPC270042
0.7234 Intermediate Similarity NPC215118
0.7234 Intermediate Similarity NPC45270
0.7234 Intermediate Similarity NPC135077
0.7234 Intermediate Similarity NPC59570
0.7143 Intermediate Similarity NPC474105
0.7143 Intermediate Similarity NPC171783
0.7045 Intermediate Similarity NPC248190
0.6786 Remote Similarity NPC319589
0.6724 Remote Similarity NPC55004
0.6724 Remote Similarity NPC49575
0.6724 Remote Similarity NPC267626
0.6721 Remote Similarity NPC472306
0.6613 Remote Similarity NPC128608
0.6613 Remote Similarity NPC473902
0.6567 Remote Similarity NPC52667
0.6567 Remote Similarity NPC248567
0.6557 Remote Similarity NPC475795
0.6522 Remote Similarity NPC121215
0.65 Remote Similarity NPC259261
0.6452 Remote Similarity NPC165695
0.6441 Remote Similarity NPC230823
0.6393 Remote Similarity NPC25853
0.6377 Remote Similarity NPC132064
0.6333 Remote Similarity NPC127798
0.6333 Remote Similarity NPC266295
0.6333 Remote Similarity NPC94991
0.6333 Remote Similarity NPC30215
0.625 Remote Similarity NPC157518
0.625 Remote Similarity NPC236623
0.6212 Remote Similarity NPC473225
0.6197 Remote Similarity NPC169389
0.6197 Remote Similarity NPC74685
0.6197 Remote Similarity NPC475932
0.619 Remote Similarity NPC32285
0.6176 Remote Similarity NPC197701
0.6176 Remote Similarity NPC311102
0.6176 Remote Similarity NPC223187
0.6154 Remote Similarity NPC39462
0.6154 Remote Similarity NPC107704
0.6154 Remote Similarity NPC43300
0.6154 Remote Similarity NPC189917
0.6154 Remote Similarity NPC96812
0.6154 Remote Similarity NPC168824
0.6129 Remote Similarity NPC66145
0.6119 Remote Similarity NPC162867
0.6119 Remote Similarity NPC477857
0.6119 Remote Similarity NPC61702
0.6119 Remote Similarity NPC474962
0.6102 Remote Similarity NPC200258
0.6102 Remote Similarity NPC307063
0.6094 Remote Similarity NPC212210
0.6061 Remote Similarity NPC475523
0.6032 Remote Similarity NPC97322
0.6032 Remote Similarity NPC213152
0.6029 Remote Similarity NPC108131
0.6029 Remote Similarity NPC307176
0.6029 Remote Similarity NPC40574
0.6 Remote Similarity NPC321646
0.6 Remote Similarity NPC168982
0.597 Remote Similarity NPC20610
0.5968 Remote Similarity NPC230070
0.5968 Remote Similarity NPC9880
0.5968 Remote Similarity NPC87828
0.5942 Remote Similarity NPC320549
0.5942 Remote Similarity NPC473267
0.5942 Remote Similarity NPC5701
0.5942 Remote Similarity NPC472309
0.5942 Remote Similarity NPC305501
0.5942 Remote Similarity NPC156277
0.5942 Remote Similarity NPC58057
0.5942 Remote Similarity NPC151018
0.5918 Remote Similarity NPC69245
0.5915 Remote Similarity NPC201263
0.5915 Remote Similarity NPC155441
0.5915 Remote Similarity NPC472311
0.5909 Remote Similarity NPC42060
0.5909 Remote Similarity NPC323005
0.5909 Remote Similarity NPC268736
0.5909 Remote Similarity NPC477931
0.5902 Remote Similarity NPC115385
0.5902 Remote Similarity NPC192427
0.589 Remote Similarity NPC228911
0.5882 Remote Similarity NPC469677
0.5882 Remote Similarity NPC327728
0.5882 Remote Similarity NPC321732
0.5882 Remote Similarity NPC213178
0.5882 Remote Similarity NPC196197
0.5882 Remote Similarity NPC139397
0.5882 Remote Similarity NPC6120
0.5882 Remote Similarity NPC182815
0.5882 Remote Similarity NPC131892
0.5882 Remote Similarity NPC324607
0.5873 Remote Similarity NPC84218
0.5857 Remote Similarity NPC303613
0.5857 Remote Similarity NPC474123
0.5857 Remote Similarity NPC310766
0.5857 Remote Similarity NPC474228
0.5857 Remote Similarity NPC232112
0.5821 Remote Similarity NPC474221
0.5821 Remote Similarity NPC478180
0.5821 Remote Similarity NPC130459
0.5797 Remote Similarity NPC151045
0.5797 Remote Similarity NPC476731
0.5797 Remote Similarity NPC2634
0.5797 Remote Similarity NPC265782
0.5797 Remote Similarity NPC35734
0.5797 Remote Similarity NPC282593
0.5797 Remote Similarity NPC159577
0.5797 Remote Similarity NPC251929
0.5797 Remote Similarity NPC477856
0.5797 Remote Similarity NPC260040
0.5797 Remote Similarity NPC246722
0.5797 Remote Similarity NPC214770
0.5789 Remote Similarity NPC116906
0.5781 Remote Similarity NPC60565
0.5781 Remote Similarity NPC83088
0.5778 Remote Similarity NPC4962
0.5778 Remote Similarity NPC79887
0.5778 Remote Similarity NPC222997
0.5778 Remote Similarity NPC221192
0.5778 Remote Similarity NPC29561
0.5778 Remote Similarity NPC196434
0.5778 Remote Similarity NPC42403
0.5778 Remote Similarity NPC153439
0.5775 Remote Similarity NPC472854
0.5775 Remote Similarity NPC159497
0.5775 Remote Similarity NPC254340
0.5775 Remote Similarity NPC133922
0.5775 Remote Similarity NPC255021
0.5763 Remote Similarity NPC474141
0.5758 Remote Similarity NPC470329
0.5758 Remote Similarity NPC469791
0.5738 Remote Similarity NPC20603
0.5733 Remote Similarity NPC279667
0.5714 Remote Similarity NPC470243
0.5714 Remote Similarity NPC89310
0.5714 Remote Similarity NPC110615
0.5714 Remote Similarity NPC470078
0.5714 Remote Similarity NPC115023
0.5714 Remote Similarity NPC13105
0.5714 Remote Similarity NPC54123
0.5714 Remote Similarity NPC126642
0.5714 Remote Similarity NPC234707
0.5714 Remote Similarity NPC143834
0.5694 Remote Similarity NPC21220
0.5694 Remote Similarity NPC72444
0.5694 Remote Similarity NPC273366
0.5694 Remote Similarity NPC195155
0.5694 Remote Similarity NPC174964
0.5694 Remote Similarity NPC125767
0.5694 Remote Similarity NPC255650
0.5694 Remote Similarity NPC97534
0.5692 Remote Similarity NPC167256
0.5682 Remote Similarity NPC100997
0.5667 Remote Similarity NPC202146
0.5667 Remote Similarity NPC202850
0.5667 Remote Similarity NPC32222
0.5667 Remote Similarity NPC63396
0.5652 Remote Similarity NPC469941
0.5652 Remote Similarity NPC476734
0.5652 Remote Similarity NPC64466
0.5652 Remote Similarity NPC252032
0.5652 Remote Similarity NPC319671
0.5645 Remote Similarity NPC193695
0.5636 Remote Similarity NPC314679
0.5634 Remote Similarity NPC251705
0.5634 Remote Similarity NPC470045
0.5634 Remote Similarity NPC92909
0.5634 Remote Similarity NPC470044
0.5634 Remote Similarity NPC107783
0.5625 Remote Similarity NPC478126
0.5616 Remote Similarity NPC472487
0.5616 Remote Similarity NPC475742
0.5616 Remote Similarity NPC5767
0.5616 Remote Similarity NPC472486
0.5616 Remote Similarity NPC69408
0.5614 Remote Similarity NPC476469
0.56 Remote Similarity NPC245029
0.56 Remote Similarity NPC90965
0.56 Remote Similarity NPC31302

  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 NPC20017 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
0.9333 High Similarity NPD344 Approved
0.9333 High Similarity NPD345 Approved
0.9333 High Similarity NPD343 Approved
0.6508 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6212 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6212 Remote Similarity NPD5360 Phase 3
0.6176 Remote Similarity NPD6081 Approved
0.6154 Remote Similarity NPD4224 Phase 2
0.6029 Remote Similarity NPD4789 Approved
0.6029 Remote Similarity NPD4747 Approved
0.5962 Remote Similarity NPD387 Clinical (unspecified phase)
0.5942 Remote Similarity NPD4758 Discontinued
0.5942 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5942 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3698 Phase 2
0.5882 Remote Similarity NPD4137 Phase 3
0.5882 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5797 Remote Similarity NPD4244 Approved
0.5797 Remote Similarity NPD4691 Approved
0.5797 Remote Similarity NPD4245 Approved
0.5775 Remote Similarity NPD5733 Approved
0.5775 Remote Similarity NPD4687 Approved
0.5735 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5777 Approved
0.5714 Remote Similarity NPD5276 Approved
0.5714 Remote Similarity NPD3198 Approved
0.5667 Remote Similarity NPD615 Clinical (unspecified phase)
0.5636 Remote Similarity NPD634 Phase 3
0.56 Remote Similarity NPD9449 Clinical (unspecified phase)

  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