Structure

Physi-Chem Properties

Molecular Weight:  152.05
Volume:  154.193
LogP:  0.602
LogD:  0.63
LogS:  -1.798
# Rotatable Bonds:  1
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.517
Synthetic Accessibility Score:  2.624
Fsp3:  0.25
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:  -4.352
MDCK Permeability:  2.772570041997824e-05
Pgp-inhibitor:  0.018
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.975
30% Bioavailability (F30%):  0.913

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.152
Plasma Protein Binding (PPB):  83.76299285888672%
Volume Distribution (VD):  1.149
Pgp-substrate:  7.908140659332275%

ADMET: Metabolism

CYP1A2-inhibitor:  0.917
CYP1A2-substrate:  0.876
CYP2C19-inhibitor:  0.591
CYP2C19-substrate:  0.663
CYP2C9-inhibitor:  0.166
CYP2C9-substrate:  0.227
CYP2D6-inhibitor:  0.456
CYP2D6-substrate:  0.146
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.269

ADMET: Excretion

Clearance (CL):  6.524
Half-life (T1/2):  0.88

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.841
Drug-inuced Liver Injury (DILI):  0.074
AMES Toxicity:  0.32
Rat Oral Acute Toxicity:  0.913
Maximum Recommended Daily Dose:  0.89
Skin Sensitization:  0.958
Carcinogencity:  0.832
Eye Corrosion:  0.847
Eye Irritation:  0.987
Respiratory Toxicity:  0.91

Download Data

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

  Natural Product: NPC220191

Natural Product ID:  NPC220191
Common Name*:   2-Methoxy-6-Methyl-1,4-Benzoquinone
IUPAC Name:   2-methoxy-6-methylcyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  HVGWDVJUMODUIZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H8O3/c1-5-3-6(9)4-7(11-2)8(5)10/h3-4H,1-2H3
SMILES:  COC1=CC(=O)C=C(C1=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL483439
PubChem CID:   101355
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 = 630.0 ug ml-1 PMID[469101]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 830.0 ug ml-1 PMID[469101]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 580.0 ug ml-1 PMID[469101]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 530.0 ug ml-1 PMID[469101]

☑ 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 NPC220191 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
0.9787 High Similarity NPC22329
0.9388 High Similarity NPC474805
0.8824 High Similarity NPC129710
0.8824 High Similarity NPC317796
0.8627 High Similarity NPC168521
0.8511 High Similarity NPC106547
0.8364 Intermediate Similarity NPC473494
0.8333 Intermediate Similarity NPC224103
0.8333 Intermediate Similarity NPC299369
0.8333 Intermediate Similarity NPC200831
0.8333 Intermediate Similarity NPC110396
0.8182 Intermediate Similarity NPC139056
0.8043 Intermediate Similarity NPC111474
0.7931 Intermediate Similarity NPC151728
0.7931 Intermediate Similarity NPC57463
0.7797 Intermediate Similarity NPC34622
0.7797 Intermediate Similarity NPC474400
0.7736 Intermediate Similarity NPC137396
0.7667 Intermediate Similarity NPC98897
0.7541 Intermediate Similarity NPC16119
0.7419 Intermediate Similarity NPC474619
0.74 Intermediate Similarity NPC477686
0.7255 Intermediate Similarity NPC166788
0.7255 Intermediate Similarity NPC191337
0.7188 Intermediate Similarity NPC262673
0.7143 Intermediate Similarity NPC251429
0.7143 Intermediate Similarity NPC243272
0.7143 Intermediate Similarity NPC298249
0.7077 Intermediate Similarity NPC94743
0.7077 Intermediate Similarity NPC291062
0.7031 Intermediate Similarity NPC125578
0.7031 Intermediate Similarity NPC263382
0.7031 Intermediate Similarity NPC146376
0.7031 Intermediate Similarity NPC134385
0.7018 Intermediate Similarity NPC25038
0.697 Remote Similarity NPC474539
0.6957 Remote Similarity NPC269641
0.6949 Remote Similarity NPC320421
0.6923 Remote Similarity NPC94488
0.6923 Remote Similarity NPC158853
0.6786 Remote Similarity NPC46565
0.6786 Remote Similarity NPC229046
0.678 Remote Similarity NPC474825
0.6774 Remote Similarity NPC477830
0.6769 Remote Similarity NPC134593
0.6765 Remote Similarity NPC264178
0.6765 Remote Similarity NPC147438
0.6739 Remote Similarity NPC12889
0.6731 Remote Similarity NPC25771
0.6727 Remote Similarity NPC15325
0.6727 Remote Similarity NPC107703
0.6727 Remote Similarity NPC118788
0.6667 Remote Similarity NPC281195
0.6667 Remote Similarity NPC475618
0.6613 Remote Similarity NPC68044
0.661 Remote Similarity NPC150717
0.66 Remote Similarity NPC101147
0.6571 Remote Similarity NPC26504
0.6557 Remote Similarity NPC203233
0.6557 Remote Similarity NPC133600
0.6538 Remote Similarity NPC292463
0.6538 Remote Similarity NPC216921
0.6522 Remote Similarity NPC266979
0.6508 Remote Similarity NPC53109
0.6508 Remote Similarity NPC143168
0.65 Remote Similarity NPC268185
0.6491 Remote Similarity NPC191643
0.6481 Remote Similarity NPC471752
0.6479 Remote Similarity NPC473536
0.6471 Remote Similarity NPC66365
0.6458 Remote Similarity NPC38497
0.6452 Remote Similarity NPC79756
0.6452 Remote Similarity NPC309408
0.6441 Remote Similarity NPC173157
0.6441 Remote Similarity NPC297280
0.6429 Remote Similarity NPC163984
0.6429 Remote Similarity NPC58970
0.6429 Remote Similarity NPC225974
0.6429 Remote Similarity NPC176819
0.6429 Remote Similarity NPC228776
0.6415 Remote Similarity NPC471753
0.6406 Remote Similarity NPC7029
0.6333 Remote Similarity NPC221763
0.6327 Remote Similarity NPC254764
0.6327 Remote Similarity NPC185839
0.6275 Remote Similarity NPC12319
0.6275 Remote Similarity NPC113082
0.6275 Remote Similarity NPC18205
0.623 Remote Similarity NPC71755
0.6226 Remote Similarity NPC301972
0.6212 Remote Similarity NPC475675
0.6212 Remote Similarity NPC475555
0.6212 Remote Similarity NPC469446
0.62 Remote Similarity NPC180840
0.6182 Remote Similarity NPC262558
0.6182 Remote Similarity NPC8610
0.6176 Remote Similarity NPC474060
0.617 Remote Similarity NPC304788
0.614 Remote Similarity NPC288381
0.614 Remote Similarity NPC20934
0.614 Remote Similarity NPC236338
0.614 Remote Similarity NPC15789
0.614 Remote Similarity NPC32351
0.6133 Remote Similarity NPC474085
0.6119 Remote Similarity NPC203335
0.6111 Remote Similarity NPC75134
0.6102 Remote Similarity NPC37644
0.6102 Remote Similarity NPC116366
0.6102 Remote Similarity NPC23117
0.6094 Remote Similarity NPC151648
0.6078 Remote Similarity NPC217923
0.6071 Remote Similarity NPC324812
0.6061 Remote Similarity NPC101670
0.6061 Remote Similarity NPC7940
0.6034 Remote Similarity NPC64866
0.6032 Remote Similarity NPC86789
0.6032 Remote Similarity NPC38455
0.6027 Remote Similarity NPC471225
0.6027 Remote Similarity NPC283087
0.6 Remote Similarity NPC270706
0.6 Remote Similarity NPC474774
0.6 Remote Similarity NPC2328
0.6 Remote Similarity NPC474658
0.6 Remote Similarity NPC218486
0.5974 Remote Similarity NPC288281
0.5968 Remote Similarity NPC283502
0.5965 Remote Similarity NPC145311
0.5965 Remote Similarity NPC234084
0.5962 Remote Similarity NPC2741
0.5938 Remote Similarity NPC130953
0.5932 Remote Similarity NPC471751
0.5921 Remote Similarity NPC99308
0.5893 Remote Similarity NPC100380
0.5893 Remote Similarity NPC128280
0.5882 Remote Similarity NPC122627
0.5873 Remote Similarity NPC311852
0.5873 Remote Similarity NPC189700
0.5862 Remote Similarity NPC275316
0.5846 Remote Similarity NPC15193
0.5846 Remote Similarity NPC263732
0.5846 Remote Similarity NPC294304
0.5846 Remote Similarity NPC228574
0.5833 Remote Similarity NPC14002
0.5833 Remote Similarity NPC296311
0.5833 Remote Similarity NPC268564
0.5823 Remote Similarity NPC8518
0.5823 Remote Similarity NPC133652
0.5823 Remote Similarity NPC241512
0.5823 Remote Similarity NPC6185
0.5823 Remote Similarity NPC132228
0.5823 Remote Similarity NPC263997
0.5821 Remote Similarity NPC182794
0.5821 Remote Similarity NPC471556
0.5821 Remote Similarity NPC476589
0.5821 Remote Similarity NPC471566
0.5821 Remote Similarity NPC471565
0.5811 Remote Similarity NPC272267
0.5806 Remote Similarity NPC86948
0.58 Remote Similarity NPC75204
0.5797 Remote Similarity NPC477117
0.5789 Remote Similarity NPC91962
0.5781 Remote Similarity NPC286189
0.5769 Remote Similarity NPC33761
0.5769 Remote Similarity NPC200147
0.5763 Remote Similarity NPC30433
0.5758 Remote Similarity NPC132243
0.5758 Remote Similarity NPC475073
0.5758 Remote Similarity NPC477707
0.5758 Remote Similarity NPC473737
0.575 Remote Similarity NPC291712
0.5741 Remote Similarity NPC187922
0.5738 Remote Similarity NPC209431
0.5738 Remote Similarity NPC5626
0.5738 Remote Similarity NPC474127
0.5738 Remote Similarity NPC300121
0.5738 Remote Similarity NPC189677
0.5738 Remote Similarity NPC478120
0.5738 Remote Similarity NPC135537
0.5738 Remote Similarity NPC100809
0.5735 Remote Similarity NPC472072
0.5735 Remote Similarity NPC137163
0.5733 Remote Similarity NPC99182
0.5714 Remote Similarity NPC281230
0.5714 Remote Similarity NPC192843
0.5714 Remote Similarity NPC474362
0.5714 Remote Similarity NPC312419
0.5714 Remote Similarity NPC474202
0.5714 Remote Similarity NPC475833
0.5696 Remote Similarity NPC469884
0.5692 Remote Similarity NPC98519
0.5692 Remote Similarity NPC429928
0.569 Remote Similarity NPC135698
0.569 Remote Similarity NPC267110
0.5686 Remote Similarity NPC24833
0.5686 Remote Similarity NPC279300
0.5676 Remote Similarity NPC477708
0.5676 Remote Similarity NPC110725
0.5672 Remote Similarity NPC150162
0.5672 Remote Similarity NPC477456
0.5672 Remote Similarity NPC477457

  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 NPC220191 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
0.8333 Intermediate Similarity NPD8779 Phase 3
0.7541 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.7347 Intermediate Similarity NPD9297 Discontinued
0.7347 Intermediate Similarity NPD9091 Suspended
0.6923 Remote Similarity NPD9090 Phase 3
0.6508 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6479 Remote Similarity NPD4756 Discovery
0.6462 Remote Similarity NPD3704 Approved
0.6078 Remote Similarity NPD5783 Phase 3
0.5921 Remote Similarity NPD5115 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9286 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9287 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