Structure

Physi-Chem Properties

Molecular Weight:  168.04
Volume:  162.983
LogP:  1.179
LogD:  0.576
LogS:  -1.375
# Rotatable Bonds:  1
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.374
Synthetic Accessibility Score:  2.892
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.053
MDCK Permeability:  1.4239878510124981e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.992
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.02
Plasma Protein Binding (PPB):  94.6103515625%
Volume Distribution (VD):  0.46
Pgp-substrate:  5.122654438018799%

ADMET: Metabolism

CYP1A2-inhibitor:  0.136
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.089
CYP2C9-substrate:  0.492
CYP2D6-inhibitor:  0.041
CYP2D6-substrate:  0.258
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.081

ADMET: Excretion

Clearance (CL):  15.687
Half-life (T1/2):  0.912

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.174
Drug-inuced Liver Injury (DILI):  0.268
AMES Toxicity:  0.65
Rat Oral Acute Toxicity:  0.098
Maximum Recommended Daily Dose:  0.709
Skin Sensitization:  0.953
Carcinogencity:  0.393
Eye Corrosion:  0.931
Eye Irritation:  0.935
Respiratory Toxicity:  0.38

Download Data

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

  Natural Product: NPC137396

Natural Product ID:  NPC137396
Common Name*:   3-Ethyl-2,5-Dihydroxycyclohexa-2,5-Diene-1,4-Dione
IUPAC Name:   3-ethyl-2,5-dihydroxycyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  WJSQCAWGGRFZJK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H8O4/c1-2-4-7(11)5(9)3-6(10)8(4)12/h3,9,12H,2H2,1H3
SMILES:  CCC1=C(C(=O)C=C(C1=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL222173
PubChem CID:   821411
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0002495] Quinones
                • [CHEMONTID:0002384] Benzoquinones
                  • [CHEMONTID:0002494] P-benzoquinones

*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
NPO146 Heliotropium indicum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO146 Heliotropium indicum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO146 Heliotropium indicum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO146 Heliotropium indicum Species Heliotropiaceae 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
NPT4309 Individual Protein Inhibitor of apoptosis protein 3 Homo sapiens Ki = 10400.0 nM PMID[494687]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 120.0 ug.mL-1 PMID[494688]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 109.0 ug.mL-1 PMID[494688]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 70.0 ug.mL-1 PMID[494688]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 62.3 ug.mL-1 PMID[494688]

☑ 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 NPC137396 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
0.8889 High Similarity NPC320421
0.8302 Intermediate Similarity NPC474805
0.8276 Intermediate Similarity NPC143168
0.8276 Intermediate Similarity NPC53109
0.8148 Intermediate Similarity NPC317796
0.8136 Intermediate Similarity NPC7029
0.7966 Intermediate Similarity NPC477830
0.7925 Intermediate Similarity NPC22329
0.7895 Intermediate Similarity NPC139056
0.7895 Intermediate Similarity NPC281195
0.7742 Intermediate Similarity NPC243272
0.7742 Intermediate Similarity NPC251429
0.7736 Intermediate Similarity NPC220191
0.7719 Intermediate Similarity NPC224103
0.7719 Intermediate Similarity NPC200831
0.7719 Intermediate Similarity NPC299369
0.7619 Intermediate Similarity NPC146376
0.7619 Intermediate Similarity NPC263382
0.7619 Intermediate Similarity NPC125578
0.75 Intermediate Similarity NPC262673
0.75 Intermediate Similarity NPC94488
0.7458 Intermediate Similarity NPC38455
0.7458 Intermediate Similarity NPC473494
0.7451 Intermediate Similarity NPC477686
0.7414 Intermediate Similarity NPC268185
0.7385 Intermediate Similarity NPC291062
0.7385 Intermediate Similarity NPC94743
0.7347 Intermediate Similarity NPC111474
0.7308 Intermediate Similarity NPC191337
0.7308 Intermediate Similarity NPC166788
0.7193 Intermediate Similarity NPC129710
0.7143 Intermediate Similarity NPC46565
0.7143 Intermediate Similarity NPC229046
0.7119 Intermediate Similarity NPC283502
0.7119 Intermediate Similarity NPC192843
0.7115 Intermediate Similarity NPC106547
0.7097 Intermediate Similarity NPC151728
0.7097 Intermediate Similarity NPC57463
0.7091 Intermediate Similarity NPC225974
0.7069 Intermediate Similarity NPC297280
0.7059 Intermediate Similarity NPC147438
0.7059 Intermediate Similarity NPC264178
0.7018 Intermediate Similarity NPC168521
0.6984 Remote Similarity NPC34622
0.6984 Remote Similarity NPC474400
0.6981 Remote Similarity NPC110396
0.697 Remote Similarity NPC474060
0.6923 Remote Similarity NPC474619
0.6923 Remote Similarity NPC298249
0.6875 Remote Similarity NPC101670
0.6875 Remote Similarity NPC98897
0.6857 Remote Similarity NPC26504
0.6833 Remote Similarity NPC281230
0.6825 Remote Similarity NPC477707
0.6818 Remote Similarity NPC134385
0.6812 Remote Similarity NPC122244
0.6792 Remote Similarity NPC471753
0.6792 Remote Similarity NPC25771
0.6786 Remote Similarity NPC118788
0.6786 Remote Similarity NPC228776
0.6786 Remote Similarity NPC15325
0.6769 Remote Similarity NPC137163
0.6769 Remote Similarity NPC16119
0.6761 Remote Similarity NPC473536
0.6667 Remote Similarity NPC158853
0.662 Remote Similarity NPC477708
0.662 Remote Similarity NPC110725
0.6618 Remote Similarity NPC107848
0.6613 Remote Similarity NPC86789
0.661 Remote Similarity NPC322461
0.6604 Remote Similarity NPC292463
0.6557 Remote Similarity NPC71755
0.6545 Remote Similarity NPC471752
0.6545 Remote Similarity NPC87137
0.6531 Remote Similarity NPC38497
0.6522 Remote Similarity NPC474539
0.6515 Remote Similarity NPC472072
0.6508 Remote Similarity NPC79756
0.6491 Remote Similarity NPC58970
0.6491 Remote Similarity NPC20934
0.6491 Remote Similarity NPC163984
0.6491 Remote Similarity NPC176819
0.6491 Remote Similarity NPC288381
0.6462 Remote Similarity NPC475618
0.6452 Remote Similarity NPC471619
0.6441 Remote Similarity NPC217188
0.6438 Remote Similarity NPC248624
0.6418 Remote Similarity NPC106613
0.6406 Remote Similarity NPC269737
0.6406 Remote Similarity NPC138056
0.6406 Remote Similarity NPC473212
0.6406 Remote Similarity NPC15130
0.6406 Remote Similarity NPC254449
0.6406 Remote Similarity NPC115752
0.6406 Remote Similarity NPC263732
0.64 Remote Similarity NPC55869
0.64 Remote Similarity NPC185839
0.6393 Remote Similarity NPC325977
0.6379 Remote Similarity NPC15129
0.6377 Remote Similarity NPC203819
0.6351 Remote Similarity NPC27817
0.6349 Remote Similarity NPC203233
0.6346 Remote Similarity NPC113082
0.6333 Remote Similarity NPC189677
0.6333 Remote Similarity NPC474127
0.6333 Remote Similarity NPC300121
0.6327 Remote Similarity NPC269641
0.6316 Remote Similarity NPC267110
0.6308 Remote Similarity NPC473211
0.6308 Remote Similarity NPC473210
0.6308 Remote Similarity NPC322457
0.6301 Remote Similarity NPC82666
0.6301 Remote Similarity NPC97173
0.6296 Remote Similarity NPC301972
0.6296 Remote Similarity NPC216921
0.6275 Remote Similarity NPC180840
0.6269 Remote Similarity NPC475555
0.6269 Remote Similarity NPC475675
0.6267 Remote Similarity NPC108955
0.625 Remote Similarity NPC175079
0.625 Remote Similarity NPC8610
0.625 Remote Similarity NPC262558
0.6234 Remote Similarity NPC105803
0.6232 Remote Similarity NPC469914
0.6232 Remote Similarity NPC136473
0.6216 Remote Similarity NPC478122
0.6212 Remote Similarity NPC150162
0.6207 Remote Similarity NPC32351
0.6207 Remote Similarity NPC107703
0.6184 Remote Similarity NPC275766
0.6176 Remote Similarity NPC269985
0.6176 Remote Similarity NPC203335
0.6176 Remote Similarity NPC122627
0.6167 Remote Similarity NPC37644
0.6164 Remote Similarity NPC1254
0.6154 Remote Similarity NPC469884
0.6154 Remote Similarity NPC260573
0.6154 Remote Similarity NPC68044
0.6154 Remote Similarity NPC64985
0.6154 Remote Similarity NPC40082
0.6143 Remote Similarity NPC173321
0.6143 Remote Similarity NPC202011
0.6143 Remote Similarity NPC318766
0.6133 Remote Similarity NPC291260
0.6122 Remote Similarity NPC12889
0.6119 Remote Similarity NPC471565
0.6119 Remote Similarity NPC471556
0.6119 Remote Similarity NPC471566
0.6111 Remote Similarity NPC160540
0.6104 Remote Similarity NPC103486
0.6104 Remote Similarity NPC47450
0.6102 Remote Similarity NPC64866
0.6102 Remote Similarity NPC477458
0.6094 Remote Similarity NPC329550
0.6094 Remote Similarity NPC106851
0.6094 Remote Similarity NPC274927
0.6094 Remote Similarity NPC133600
0.6087 Remote Similarity NPC309466
0.6081 Remote Similarity NPC272267
0.6076 Remote Similarity NPC474680
0.6076 Remote Similarity NPC32037
0.6076 Remote Similarity NPC77971
0.6076 Remote Similarity NPC8518
0.6076 Remote Similarity NPC241512
0.6076 Remote Similarity NPC263997
0.6076 Remote Similarity NPC6185
0.6076 Remote Similarity NPC132228
0.6076 Remote Similarity NPC470177
0.6071 Remote Similarity NPC117572
0.6071 Remote Similarity NPC474362
0.6071 Remote Similarity NPC474202
0.6066 Remote Similarity NPC154626
0.6061 Remote Similarity NPC474774
0.6061 Remote Similarity NPC190049
0.6061 Remote Similarity NPC68110
0.6056 Remote Similarity NPC474884
0.6053 Remote Similarity NPC74086
0.6038 Remote Similarity NPC101147
0.6034 Remote Similarity NPC145311
0.6034 Remote Similarity NPC122212
0.6034 Remote Similarity NPC137419
0.6034 Remote Similarity NPC313553
0.6029 Remote Similarity NPC100719
0.6029 Remote Similarity NPC322035
0.6029 Remote Similarity NPC197089
0.6029 Remote Similarity NPC166791
0.6027 Remote Similarity NPC474885
0.6 Remote Similarity NPC122521
0.6 Remote Similarity NPC174447
0.6 Remote Similarity NPC30321
0.6 Remote Similarity NPC235242
0.6 Remote Similarity NPC471751
0.6 Remote Similarity NPC231739
0.6 Remote Similarity NPC251042
0.5974 Remote Similarity NPC99308
0.5974 Remote Similarity NPC225515
0.5972 Remote Similarity NPC153660
0.5972 Remote Similarity NPC215745
0.5972 Remote Similarity NPC238948
0.5972 Remote Similarity NPC12815

  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 NPC137396 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
0.8276 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7719 Intermediate Similarity NPD8779 Phase 3
0.7031 Intermediate Similarity NPD3704 Approved
0.6769 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6761 Remote Similarity NPD4756 Discovery
0.6667 Remote Similarity NPD9090 Phase 3
0.6557 Remote Similarity NPD9287 Clinical (unspecified phase)
0.6486 Remote Similarity NPD4695 Discontinued
0.6393 Remote Similarity NPD9286 Clinical (unspecified phase)
0.6296 Remote Similarity NPD9411 Phase 1
0.6269 Remote Similarity NPD7331 Phase 2
0.6154 Remote Similarity NPD5783 Phase 3
0.6111 Remote Similarity NPD9297 Discontinued
0.6111 Remote Similarity NPD9091 Suspended
0.6071 Remote Similarity NPD4222 Approved
0.6053 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5968 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5882 Remote Similarity NPD7341 Phase 2
0.5823 Remote Similarity NPD6110 Phase 1
0.5806 Remote Similarity NPD539 Approved
0.5789 Remote Similarity NPD39 Approved
0.5763 Remote Similarity NPD3173 Approved
0.5714 Remote Similarity NPD5326 Phase 3
0.5692 Remote Similarity NPD9306 Approved
0.5692 Remote Similarity NPD6109 Phase 1
0.5679 Remote Similarity NPD1696 Phase 3

  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