Structure

Physi-Chem Properties

Molecular Weight:  194.09
Volume:  206.081
LogP:  2.953
LogD:  2.747
LogS:  -2.301
# Rotatable Bonds:  3
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.727
Synthetic Accessibility Score:  2.479
Fsp3:  0.273
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:  -4.677
MDCK Permeability:  2.178380782424938e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.3
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.165

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.096
Plasma Protein Binding (PPB):  96.27098846435547%
Volume Distribution (VD):  1.229
Pgp-substrate:  3.732438325881958%

ADMET: Metabolism

CYP1A2-inhibitor:  0.9
CYP1A2-substrate:  0.924
CYP2C19-inhibitor:  0.161
CYP2C19-substrate:  0.568
CYP2C9-inhibitor:  0.102
CYP2C9-substrate:  0.917
CYP2D6-inhibitor:  0.362
CYP2D6-substrate:  0.915
CYP3A4-inhibitor:  0.109
CYP3A4-substrate:  0.206

ADMET: Excretion

Clearance (CL):  13.571
Half-life (T1/2):  0.903

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.115
Drug-inuced Liver Injury (DILI):  0.024
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.356
Maximum Recommended Daily Dose:  0.444
Skin Sensitization:  0.955
Carcinogencity:  0.408
Eye Corrosion:  0.748
Eye Irritation:  0.968
Respiratory Toxicity:  0.613

Download Data

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

  Natural Product: NPC473494

Natural Product ID:  NPC473494
Common Name*:   2-Methoxy-6-Butyl-1,4-Benzoquinone
IUPAC Name:   2-butyl-6-methoxycyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  JTNZEYFXPDFBBF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H14O3/c1-3-4-5-8-6-9(12)7-10(14-2)11(8)13/h6-7H,3-5H2,1-2H3
SMILES:  CCCCC1=CC(=O)C=C(C1=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443690
PubChem CID:   3017085
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
NPT179 Cell Line A2780 Homo sapiens IC50 = 3.2 ug.mL-1 PMID[465696]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 220.0 ug ml-1 PMID[465696]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 210.0 ug ml-1 PMID[465696]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 80.0 ug ml-1 PMID[465696]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 150.0 ug ml-1 PMID[465696]

☑ 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 NPC473494 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
0.9483 High Similarity NPC57463
0.9483 High Similarity NPC151728
0.9322 High Similarity NPC34622
0.9322 High Similarity NPC474400
0.9167 High Similarity NPC98897
0.9016 High Similarity NPC16119
0.8909 High Similarity NPC474805
0.8871 High Similarity NPC474619
0.8793 High Similarity NPC139056
0.8594 High Similarity NPC262673
0.8571 High Similarity NPC243272
0.8475 Intermediate Similarity NPC320421
0.8462 Intermediate Similarity NPC94743
0.8462 Intermediate Similarity NPC291062
0.8438 Intermediate Similarity NPC146376
0.8438 Intermediate Similarity NPC263382
0.8438 Intermediate Similarity NPC134385
0.8438 Intermediate Similarity NPC125578
0.8421 Intermediate Similarity NPC317796
0.8364 Intermediate Similarity NPC220191
0.8308 Intermediate Similarity NPC94488
0.8226 Intermediate Similarity NPC477830
0.8214 Intermediate Similarity NPC22329
0.8088 Intermediate Similarity NPC264178
0.8 Intermediate Similarity NPC200831
0.8 Intermediate Similarity NPC299369
0.8 Intermediate Similarity NPC224103
0.7937 Intermediate Similarity NPC53109
0.7937 Intermediate Similarity NPC143168
0.7812 Intermediate Similarity NPC7029
0.7746 Intermediate Similarity NPC473536
0.7727 Intermediate Similarity NPC251429
0.7727 Intermediate Similarity NPC298249
0.75 Intermediate Similarity NPC129710
0.7458 Intermediate Similarity NPC137396
0.7455 Intermediate Similarity NPC25771
0.7333 Intermediate Similarity NPC168521
0.7333 Intermediate Similarity NPC474085
0.7286 Intermediate Similarity NPC474539
0.7273 Intermediate Similarity NPC292463
0.726 Intermediate Similarity NPC283087
0.7143 Intermediate Similarity NPC106547
0.7121 Intermediate Similarity NPC477707
0.7083 Intermediate Similarity NPC147438
0.7018 Intermediate Similarity NPC191337
0.7018 Intermediate Similarity NPC110396
0.6962 Remote Similarity NPC6185
0.6962 Remote Similarity NPC8518
0.6962 Remote Similarity NPC263997
0.6962 Remote Similarity NPC132228
0.6962 Remote Similarity NPC133652
0.6962 Remote Similarity NPC241512
0.6892 Remote Similarity NPC26504
0.6892 Remote Similarity NPC477708
0.6842 Remote Similarity NPC477686
0.6833 Remote Similarity NPC176819
0.6833 Remote Similarity NPC15325
0.6833 Remote Similarity NPC32351
0.6833 Remote Similarity NPC163984
0.6833 Remote Similarity NPC58970
0.6818 Remote Similarity NPC229252
0.6818 Remote Similarity NPC143857
0.6795 Remote Similarity NPC47450
0.678 Remote Similarity NPC324812
0.6761 Remote Similarity NPC474060
0.675 Remote Similarity NPC475614
0.675 Remote Similarity NPC2640
0.6727 Remote Similarity NPC111474
0.6724 Remote Similarity NPC166788
0.6721 Remote Similarity NPC64866
0.6716 Remote Similarity NPC68044
0.6711 Remote Similarity NPC23778
0.6667 Remote Similarity NPC145311
0.6667 Remote Similarity NPC474353
0.662 Remote Similarity NPC134593
0.6615 Remote Similarity NPC192843
0.6615 Remote Similarity NPC281230
0.6613 Remote Similarity NPC471751
0.661 Remote Similarity NPC471752
0.6579 Remote Similarity NPC272267
0.6579 Remote Similarity NPC471225
0.6571 Remote Similarity NPC472072
0.6557 Remote Similarity NPC228776
0.6548 Remote Similarity NPC223093
0.6543 Remote Similarity NPC470177
0.6543 Remote Similarity NPC77971
0.6538 Remote Similarity NPC304795
0.6538 Remote Similarity NPC108955
0.6528 Remote Similarity NPC469914
0.6515 Remote Similarity NPC281195
0.6515 Remote Similarity NPC311852
0.6508 Remote Similarity NPC268564
0.65 Remote Similarity NPC91962
0.65 Remote Similarity NPC288281
0.6494 Remote Similarity NPC231739
0.6494 Remote Similarity NPC478247
0.6494 Remote Similarity NPC478246
0.6479 Remote Similarity NPC203335
0.6471 Remote Similarity NPC476484
0.6471 Remote Similarity NPC193396
0.6471 Remote Similarity NPC32944
0.6463 Remote Similarity NPC203795
0.6463 Remote Similarity NPC472009
0.6456 Remote Similarity NPC286229
0.6456 Remote Similarity NPC55869
0.6456 Remote Similarity NPC99308
0.6447 Remote Similarity NPC470525
0.6447 Remote Similarity NPC473223
0.6447 Remote Similarity NPC110725
0.6447 Remote Similarity NPC40353
0.6438 Remote Similarity NPC477455
0.6438 Remote Similarity NPC173321
0.6429 Remote Similarity NPC113082
0.6429 Remote Similarity NPC142159
0.6429 Remote Similarity NPC95364
0.642 Remote Similarity NPC469809
0.6418 Remote Similarity NPC274927
0.6418 Remote Similarity NPC106851
0.641 Remote Similarity NPC471740
0.641 Remote Similarity NPC476177
0.641 Remote Similarity NPC475681
0.6406 Remote Similarity NPC209431
0.6406 Remote Similarity NPC100809
0.64 Remote Similarity NPC215050
0.64 Remote Similarity NPC122244
0.6389 Remote Similarity NPC218477
0.6386 Remote Similarity NPC472007
0.6379 Remote Similarity NPC301972
0.6377 Remote Similarity NPC474774
0.6375 Remote Similarity NPC103486
0.6364 Remote Similarity NPC471061
0.6364 Remote Similarity NPC41780
0.6364 Remote Similarity NPC180290
0.6364 Remote Similarity NPC211279
0.6364 Remote Similarity NPC187568
0.6364 Remote Similarity NPC268185
0.6353 Remote Similarity NPC475823
0.6353 Remote Similarity NPC474209
0.6351 Remote Similarity NPC66365
0.6349 Remote Similarity NPC216407
0.6341 Remote Similarity NPC32037
0.6341 Remote Similarity NPC474680
0.6341 Remote Similarity NPC281172
0.6338 Remote Similarity NPC248125
0.6338 Remote Similarity NPC137163
0.6338 Remote Similarity NPC197089
0.6338 Remote Similarity NPC322035
0.6338 Remote Similarity NPC166791
0.6338 Remote Similarity NPC100719
0.6338 Remote Similarity NPC469446
0.6333 Remote Similarity NPC262558
0.6333 Remote Similarity NPC100380
0.6333 Remote Similarity NPC8610
0.6329 Remote Similarity NPC91332
0.6329 Remote Similarity NPC162741
0.6324 Remote Similarity NPC79756
0.6324 Remote Similarity NPC122521
0.6324 Remote Similarity NPC235242
0.6324 Remote Similarity NPC174447
0.6324 Remote Similarity NPC429928
0.6324 Remote Similarity NPC251042
0.631 Remote Similarity NPC53454
0.631 Remote Similarity NPC472008
0.6301 Remote Similarity NPC477448
0.6301 Remote Similarity NPC477449
0.6301 Remote Similarity NPC10758
0.6301 Remote Similarity NPC250928
0.6296 Remote Similarity NPC8091
0.629 Remote Similarity NPC118788
0.6286 Remote Similarity NPC477456
0.6286 Remote Similarity NPC477457
0.6286 Remote Similarity NPC150162
0.6282 Remote Similarity NPC475994
0.6282 Remote Similarity NPC248624
0.6282 Remote Similarity NPC478122
0.6279 Remote Similarity NPC166110
0.6267 Remote Similarity NPC472956
0.6267 Remote Similarity NPC186042
0.625 Remote Similarity NPC475833
0.625 Remote Similarity NPC275766
0.625 Remote Similarity NPC296311
0.625 Remote Similarity NPC309606
0.625 Remote Similarity NPC45283
0.625 Remote Similarity NPC159714
0.625 Remote Similarity NPC478262
0.625 Remote Similarity NPC149237
0.625 Remote Similarity NPC269985
0.625 Remote Similarity NPC139545
0.625 Remote Similarity NPC39633
0.625 Remote Similarity NPC221510
0.625 Remote Similarity NPC225515
0.625 Remote Similarity NPC37644
0.6235 Remote Similarity NPC280833
0.6232 Remote Similarity NPC151648
0.6232 Remote Similarity NPC40082
0.622 Remote Similarity NPC474251
0.622 Remote Similarity NPC469884
0.622 Remote Similarity NPC474359
0.6216 Remote Similarity NPC107848
0.6212 Remote Similarity NPC473733

  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 NPC473494 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
0.9016 High Similarity NPD6108 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD8779 Phase 3
0.7937 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7846 Intermediate Similarity NPD3704 Approved
0.7746 Intermediate Similarity NPD4756 Discovery
0.6571 Remote Similarity NPD7331 Phase 2
0.6538 Remote Similarity NPD4695 Discontinued
0.6207 Remote Similarity NPD9091 Suspended
0.6207 Remote Similarity NPD9297 Discontinued
0.6098 Remote Similarity NPD6110 Phase 1
0.6061 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6029 Remote Similarity NPD287 Approved
0.5972 Remote Similarity NPD7341 Phase 2
0.5938 Remote Similarity NPD28 Approved
0.5938 Remote Similarity NPD29 Approved
0.593 Remote Similarity NPD5737 Approved
0.593 Remote Similarity NPD6672 Approved
0.5926 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5902 Remote Similarity NPD3174 Discontinued
0.5902 Remote Similarity NPD9090 Phase 3
0.5833 Remote Similarity NPD3197 Phase 1
0.5778 Remote Similarity NPD5282 Discontinued
0.5765 Remote Similarity NPD1696 Phase 3
0.5758 Remote Similarity NPD3172 Approved
0.5698 Remote Similarity NPD5279 Phase 3
0.5698 Remote Similarity NPD5690 Phase 2
0.569 Remote Similarity NPD5783 Phase 3
0.5682 Remote Similarity NPD6904 Approved
0.5682 Remote Similarity NPD6080 Approved
0.5682 Remote Similarity NPD6673 Approved
0.5679 Remote Similarity NPD3617 Approved
0.5672 Remote Similarity NPD3194 Approved
0.5672 Remote Similarity NPD3196 Approved
0.5672 Remote Similarity NPD4266 Approved
0.5672 Remote Similarity NPD3195 Phase 2
0.5647 Remote Similarity NPD4197 Approved
0.5625 Remote Similarity NPD3173 Approved
0.5618 Remote Similarity NPD5692 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