Structure

Physi-Chem Properties

Molecular Weight:  166.06
Volume:  171.489
LogP:  1.934
LogD:  1.595
LogS:  -1.454
# Rotatable Bonds:  2
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.658
Synthetic Accessibility Score:  2.456
Fsp3:  0.111
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.609
MDCK Permeability:  2.034422504948452e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.014
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.063
30% Bioavailability (F30%):  0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.063
Plasma Protein Binding (PPB):  89.42964172363281%
Volume Distribution (VD):  0.671
Pgp-substrate:  8.189809799194336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.7
CYP1A2-substrate:  0.816
CYP2C19-inhibitor:  0.058
CYP2C19-substrate:  0.383
CYP2C9-inhibitor:  0.052
CYP2C9-substrate:  0.887
CYP2D6-inhibitor:  0.118
CYP2D6-substrate:  0.889
CYP3A4-inhibitor:  0.035
CYP3A4-substrate:  0.198

ADMET: Excretion

Clearance (CL):  14.597
Half-life (T1/2):  0.905

ADMET: Toxicity

hERG Blockers:  0.041
Human Hepatotoxicity (H-HT):  0.089
Drug-inuced Liver Injury (DILI):  0.133
AMES Toxicity:  0.071
Rat Oral Acute Toxicity:  0.604
Maximum Recommended Daily Dose:  0.828
Skin Sensitization:  0.924
Carcinogencity:  0.425
Eye Corrosion:  0.937
Eye Irritation:  0.976
Respiratory Toxicity:  0.62

Download Data

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

  Natural Product: NPC474805

Natural Product ID:  NPC474805
Common Name*:   2-Methoxy-6-Ethyl-1,4-Benzoquinone
IUPAC Name:   2-ethyl-6-methoxycyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  LZTWXXJTDLQTAT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H10O3/c1-3-6-4-7(10)5-8(12-2)9(6)11/h4-5H,3H2,1-2H3
SMILES:  CCC1=CC(=O)C=C(C1=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL483440
PubChem CID:   21592367
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
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. Suriname rainforest n.a. PMID[11170656]
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[11170656]
NPO25763 Miconia lepidota Species Melastomataceae 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
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 220.0 ug ml-1 PMID[521367]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 200.0 ug ml-1 PMID[521367]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 233.0 ug ml-1 PMID[521367]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 140.0 ug ml-1 PMID[521367]

☑ 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 NPC474805 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
0.9412 High Similarity NPC317796
0.9388 High Similarity NPC220191
0.92 High Similarity NPC22329
0.8909 High Similarity NPC473494
0.8889 High Similarity NPC224103
0.8889 High Similarity NPC299369
0.8889 High Similarity NPC200831
0.8727 High Similarity NPC139056
0.8448 Intermediate Similarity NPC57463
0.8448 Intermediate Similarity NPC151728
0.8333 Intermediate Similarity NPC129710
0.8305 Intermediate Similarity NPC34622
0.8305 Intermediate Similarity NPC474400
0.8302 Intermediate Similarity NPC137396
0.8167 Intermediate Similarity NPC98897
0.8148 Intermediate Similarity NPC168521
0.8033 Intermediate Similarity NPC16119
0.8 Intermediate Similarity NPC106547
0.7903 Intermediate Similarity NPC474619
0.7843 Intermediate Similarity NPC110396
0.7656 Intermediate Similarity NPC262673
0.7647 Intermediate Similarity NPC477686
0.7619 Intermediate Similarity NPC243272
0.7619 Intermediate Similarity NPC298249
0.7619 Intermediate Similarity NPC251429
0.7551 Intermediate Similarity NPC111474
0.7538 Intermediate Similarity NPC94743
0.7538 Intermediate Similarity NPC291062
0.75 Intermediate Similarity NPC146376
0.75 Intermediate Similarity NPC166788
0.75 Intermediate Similarity NPC263382
0.75 Intermediate Similarity NPC134385
0.75 Intermediate Similarity NPC125578
0.75 Intermediate Similarity NPC191337
0.7458 Intermediate Similarity NPC320421
0.7424 Intermediate Similarity NPC474539
0.7385 Intermediate Similarity NPC94488
0.7258 Intermediate Similarity NPC477830
0.7206 Intermediate Similarity NPC264178
0.7206 Intermediate Similarity NPC147438
0.7167 Intermediate Similarity NPC281195
0.7 Intermediate Similarity NPC268185
0.7 Intermediate Similarity NPC26504
0.6984 Remote Similarity NPC53109
0.6984 Remote Similarity NPC143168
0.6981 Remote Similarity NPC25771
0.6964 Remote Similarity NPC15325
0.6964 Remote Similarity NPC118788
0.6935 Remote Similarity NPC79756
0.6901 Remote Similarity NPC473536
0.6875 Remote Similarity NPC7029
0.6825 Remote Similarity NPC68044
0.6792 Remote Similarity NPC292463
0.6774 Remote Similarity NPC133600
0.6774 Remote Similarity NPC203233
0.6735 Remote Similarity NPC38497
0.6727 Remote Similarity NPC471752
0.6716 Remote Similarity NPC134593
0.6667 Remote Similarity NPC58970
0.6667 Remote Similarity NPC225974
0.6667 Remote Similarity NPC176819
0.6667 Remote Similarity NPC228776
0.6667 Remote Similarity NPC471753
0.6667 Remote Similarity NPC25038
0.6667 Remote Similarity NPC163984
0.6615 Remote Similarity NPC475618
0.66 Remote Similarity NPC185839
0.6567 Remote Similarity NPC203335
0.6562 Remote Similarity NPC151648
0.6545 Remote Similarity NPC158853
0.6538 Remote Similarity NPC101147
0.6538 Remote Similarity NPC113082
0.6533 Remote Similarity NPC474085
0.6531 Remote Similarity NPC269641
0.6515 Remote Similarity NPC101670
0.6508 Remote Similarity NPC38455
0.6481 Remote Similarity NPC301972
0.6481 Remote Similarity NPC216921
0.6471 Remote Similarity NPC180840
0.6462 Remote Similarity NPC474658
0.6462 Remote Similarity NPC474774
0.6452 Remote Similarity NPC474825
0.6441 Remote Similarity NPC229046
0.6441 Remote Similarity NPC46565
0.6438 Remote Similarity NPC283087
0.6429 Remote Similarity NPC262558
0.6429 Remote Similarity NPC66365
0.6429 Remote Similarity NPC8610
0.6418 Remote Similarity NPC469446
0.6406 Remote Similarity NPC309408
0.6393 Remote Similarity NPC297280
0.6393 Remote Similarity NPC173157
0.6379 Remote Similarity NPC32351
0.6379 Remote Similarity NPC107703
0.6377 Remote Similarity NPC474060
0.6333 Remote Similarity NPC37644
0.6327 Remote Similarity NPC12889
0.6316 Remote Similarity NPC324812
0.629 Remote Similarity NPC150717
0.6271 Remote Similarity NPC64866
0.6226 Remote Similarity NPC18205
0.6226 Remote Similarity NPC12319
0.6216 Remote Similarity NPC471225
0.6216 Remote Similarity NPC272267
0.6212 Remote Similarity NPC477707
0.6207 Remote Similarity NPC145311
0.6203 Remote Similarity NPC6185
0.6203 Remote Similarity NPC8518
0.6203 Remote Similarity NPC133652
0.6203 Remote Similarity NPC263997
0.6203 Remote Similarity NPC132228
0.6203 Remote Similarity NPC241512
0.619 Remote Similarity NPC281230
0.619 Remote Similarity NPC71755
0.619 Remote Similarity NPC192843
0.619 Remote Similarity NPC283502
0.6176 Remote Similarity NPC472072
0.6176 Remote Similarity NPC137163
0.6167 Remote Similarity NPC471751
0.6167 Remote Similarity NPC191643
0.6154 Remote Similarity NPC288281
0.614 Remote Similarity NPC100380
0.6125 Remote Similarity NPC291712
0.6122 Remote Similarity NPC266979
0.6104 Remote Similarity NPC99308
0.6102 Remote Similarity NPC288381
0.6102 Remote Similarity NPC20934
0.6102 Remote Similarity NPC236338
0.6094 Remote Similarity NPC311852
0.6087 Remote Similarity NPC122627
0.6087 Remote Similarity NPC106613
0.6081 Remote Similarity NPC477708
0.6081 Remote Similarity NPC110725
0.6076 Remote Similarity NPC469884
0.6066 Remote Similarity NPC296311
0.6066 Remote Similarity NPC268564
0.6066 Remote Similarity NPC217188
0.6066 Remote Similarity NPC23117
0.6061 Remote Similarity NPC15193
0.6061 Remote Similarity NPC228574
0.6061 Remote Similarity NPC294304
0.6061 Remote Similarity NPC269737
0.6056 Remote Similarity NPC107848
0.6053 Remote Similarity NPC291260
0.6038 Remote Similarity NPC217923
0.6034 Remote Similarity NPC91962
0.6032 Remote Similarity NPC86948
0.6032 Remote Similarity NPC221763
0.6029 Remote Similarity NPC7940
0.6029 Remote Similarity NPC471556
0.6029 Remote Similarity NPC182794
0.6029 Remote Similarity NPC471565
0.6029 Remote Similarity NPC471566
0.6027 Remote Similarity NPC122244
0.6026 Remote Similarity NPC47450
0.6 Remote Similarity NPC281172
0.6 Remote Similarity NPC475614
0.6 Remote Similarity NPC86789
0.6 Remote Similarity NPC30433
0.6 Remote Similarity NPC287705
0.6 Remote Similarity NPC77971
0.6 Remote Similarity NPC470256
0.6 Remote Similarity NPC2640
0.5972 Remote Similarity NPC133098
0.597 Remote Similarity NPC132243
0.597 Remote Similarity NPC2328
0.5968 Remote Similarity NPC189677
0.5968 Remote Similarity NPC300121
0.5968 Remote Similarity NPC322461
0.5968 Remote Similarity NPC209431
0.5968 Remote Similarity NPC100809
0.5965 Remote Similarity NPC270706
0.5962 Remote Similarity NPC254764
0.5962 Remote Similarity NPC24833
0.5942 Remote Similarity NPC248125
0.5942 Remote Similarity NPC475555
0.5942 Remote Similarity NPC475675
0.5932 Remote Similarity NPC267110
0.5932 Remote Similarity NPC135698
0.5921 Remote Similarity NPC23778
0.5921 Remote Similarity NPC99182
0.5921 Remote Similarity NPC469510
0.5915 Remote Similarity NPC473603
0.5915 Remote Similarity NPC476591
0.5915 Remote Similarity NPC88877
0.5915 Remote Similarity NPC476059
0.5909 Remote Similarity NPC429928
0.5909 Remote Similarity NPC143857
0.5909 Remote Similarity NPC229252
0.5902 Remote Similarity NPC216407
0.5902 Remote Similarity NPC170167
0.5897 Remote Similarity NPC312419
0.5897 Remote Similarity NPC475833
0.5897 Remote Similarity NPC474353
0.5882 Remote Similarity NPC477457
0.5882 Remote Similarity NPC477456
0.5882 Remote Similarity NPC150162
0.5875 Remote Similarity NPC469809
0.5862 Remote Similarity NPC128280
0.5857 Remote Similarity NPC269985

  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 NPC474805 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
0.8889 High Similarity NPD8779 Phase 3
0.8033 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.6984 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6923 Remote Similarity NPD9297 Discontinued
0.6923 Remote Similarity NPD9091 Suspended
0.6923 Remote Similarity NPD3704 Approved
0.6901 Remote Similarity NPD4756 Discovery
0.6545 Remote Similarity NPD9090 Phase 3
0.6346 Remote Similarity NPD5783 Phase 3
0.5949 Remote Similarity NPD6110 Phase 1
0.5846 Remote Similarity NPD6109 Phase 1
0.5769 Remote Similarity NPD4695 Discontinued
0.5763 Remote Similarity NPD5343 Approved
0.5738 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD7331 Phase 2
0.5696 Remote Similarity NPD5115 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5606 Remote Similarity NPD287 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