Structure

Physi-Chem Properties

Molecular Weight:  236.14
Volume:  257.969
LogP:  4.084
LogD:  3.687
LogS:  -3.65
# Rotatable Bonds:  6
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.585
Synthetic Accessibility Score:  2.335
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.779
MDCK Permeability:  2.6218865968985483e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.192
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.839
30% Bioavailability (F30%):  0.335

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.101
Plasma Protein Binding (PPB):  97.8277359008789%
Volume Distribution (VD):  3.653
Pgp-substrate:  2.396178722381592%

ADMET: Metabolism

CYP1A2-inhibitor:  0.973
CYP1A2-substrate:  0.927
CYP2C19-inhibitor:  0.806
CYP2C19-substrate:  0.592
CYP2C9-inhibitor:  0.532
CYP2C9-substrate:  0.943
CYP2D6-inhibitor:  0.755
CYP2D6-substrate:  0.921
CYP3A4-inhibitor:  0.408
CYP3A4-substrate:  0.151

ADMET: Excretion

Clearance (CL):  11.133
Half-life (T1/2):  0.875

ADMET: Toxicity

hERG Blockers:  0.041
Human Hepatotoxicity (H-HT):  0.07
Drug-inuced Liver Injury (DILI):  0.025
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.318
Maximum Recommended Daily Dose:  0.485
Skin Sensitization:  0.963
Carcinogencity:  0.218
Eye Corrosion:  0.784
Eye Irritation:  0.971
Respiratory Toxicity:  0.781

Download Data

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

  Natural Product: NPC151728

Natural Product ID:  NPC151728
Common Name*:   2-Methoxy-6-Heptyl-1,4-Benzoquinone
IUPAC Name:   2-heptyl-6-methoxycyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  FVLYRFSEEUSOAL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H20O3/c1-3-4-5-6-7-8-11-9-12(15)10-13(17-2)14(11)16/h9-10H,3-8H2,1-2H3
SMILES:  CCCCCCCC1=CC(=O)C=C(C1=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL447771
PubChem CID:   183882
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 = 7.9 ug.mL-1 PMID[473677]
NPT726 Cell Line M109 Mus musculus IC50 = 10.0 ug.mL-1 PMID[473677]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 220.0 ug ml-1 PMID[473677]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 130.0 ug ml-1 PMID[473677]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 120.0 ug ml-1 PMID[473677]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 16.0 ug ml-1 PMID[473677]

☑ 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 NPC151728 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
1.0 High Similarity NPC57463
0.9831 High Similarity NPC474400
0.9831 High Similarity NPC34622
0.9667 High Similarity NPC98897
0.9508 High Similarity NPC16119
0.9483 High Similarity NPC473494
0.9355 High Similarity NPC474619
0.9062 High Similarity NPC262673
0.9048 High Similarity NPC243272
0.8923 High Similarity NPC94743
0.8923 High Similarity NPC291062
0.8906 High Similarity NPC125578
0.8906 High Similarity NPC134385
0.8906 High Similarity NPC146376
0.8906 High Similarity NPC263382
0.8769 High Similarity NPC94488
0.871 High Similarity NPC477830
0.8529 High Similarity NPC264178
0.8448 Intermediate Similarity NPC474805
0.8413 Intermediate Similarity NPC53109
0.8413 Intermediate Similarity NPC143168
0.8361 Intermediate Similarity NPC139056
0.8305 Intermediate Similarity NPC317796
0.8281 Intermediate Similarity NPC7029
0.8169 Intermediate Similarity NPC473536
0.8065 Intermediate Similarity NPC320421
0.7931 Intermediate Similarity NPC220191
0.7903 Intermediate Similarity NPC299369
0.7903 Intermediate Similarity NPC200831
0.7903 Intermediate Similarity NPC224103
0.7797 Intermediate Similarity NPC22329
0.7733 Intermediate Similarity NPC474085
0.7671 Intermediate Similarity NPC283087
0.7576 Intermediate Similarity NPC477707
0.7465 Intermediate Similarity NPC474539
0.7391 Intermediate Similarity NPC298249
0.7391 Intermediate Similarity NPC251429
0.7342 Intermediate Similarity NPC8518
0.7342 Intermediate Similarity NPC263997
0.7342 Intermediate Similarity NPC133652
0.7342 Intermediate Similarity NPC6185
0.7342 Intermediate Similarity NPC132228
0.7342 Intermediate Similarity NPC241512
0.7297 Intermediate Similarity NPC477708
0.7273 Intermediate Similarity NPC143857
0.7273 Intermediate Similarity NPC229252
0.726 Intermediate Similarity NPC147438
0.7167 Intermediate Similarity NPC145311
0.7143 Intermediate Similarity NPC129710
0.7105 Intermediate Similarity NPC23778
0.7097 Intermediate Similarity NPC137396
0.7069 Intermediate Similarity NPC25771
0.7067 Intermediate Similarity NPC26504
0.7051 Intermediate Similarity NPC474353
0.6984 Remote Similarity NPC168521
0.6962 Remote Similarity NPC47450
0.6949 Remote Similarity NPC191337
0.6944 Remote Similarity NPC469914
0.6944 Remote Similarity NPC474060
0.6923 Remote Similarity NPC304795
0.6923 Remote Similarity NPC108955
0.6905 Remote Similarity NPC223093
0.6897 Remote Similarity NPC292463
0.6883 Remote Similarity NPC478246
0.6883 Remote Similarity NPC231739
0.6883 Remote Similarity NPC478247
0.6866 Remote Similarity NPC106851
0.6866 Remote Similarity NPC274927
0.6849 Remote Similarity NPC173321
0.6849 Remote Similarity NPC477455
0.6842 Remote Similarity NPC470525
0.6842 Remote Similarity NPC40353
0.6842 Remote Similarity NPC473223
0.6842 Remote Similarity NPC110725
0.6835 Remote Similarity NPC55869
0.6835 Remote Similarity NPC99308
0.6835 Remote Similarity NPC286229
0.6829 Remote Similarity NPC472009
0.6829 Remote Similarity NPC203795
0.6824 Remote Similarity NPC32944
0.6824 Remote Similarity NPC193396
0.6818 Remote Similarity NPC192843
0.6818 Remote Similarity NPC281230
0.6806 Remote Similarity NPC218477
0.6806 Remote Similarity NPC134593
0.6795 Remote Similarity NPC476177
0.6795 Remote Similarity NPC471740
0.6795 Remote Similarity NPC475681
0.6786 Remote Similarity NPC95364
0.6786 Remote Similarity NPC142159
0.678 Remote Similarity NPC477686
0.678 Remote Similarity NPC106547
0.6774 Remote Similarity NPC32351
0.6774 Remote Similarity NPC15325
0.6765 Remote Similarity NPC122521
0.6765 Remote Similarity NPC235242
0.6765 Remote Similarity NPC251042
0.6765 Remote Similarity NPC174447
0.6761 Remote Similarity NPC197089
0.6753 Remote Similarity NPC211279
0.6753 Remote Similarity NPC180290
0.6753 Remote Similarity NPC41780
0.6753 Remote Similarity NPC187568
0.6753 Remote Similarity NPC471061
0.675 Remote Similarity NPC103486
0.6747 Remote Similarity NPC472007
0.6719 Remote Similarity NPC139545
0.6719 Remote Similarity NPC39633
0.6719 Remote Similarity NPC309606
0.6714 Remote Similarity NPC150162
0.6712 Remote Similarity NPC477449
0.6712 Remote Similarity NPC477448
0.6712 Remote Similarity NPC10758
0.6712 Remote Similarity NPC250928
0.6707 Remote Similarity NPC474680
0.6707 Remote Similarity NPC470177
0.6707 Remote Similarity NPC32037
0.6707 Remote Similarity NPC77971
0.6706 Remote Similarity NPC475823
0.6706 Remote Similarity NPC474209
0.6667 Remote Similarity NPC110396
0.6667 Remote Similarity NPC475994
0.6667 Remote Similarity NPC53454
0.6667 Remote Similarity NPC40082
0.6667 Remote Similarity NPC234829
0.6667 Remote Similarity NPC288281
0.6667 Remote Similarity NPC477458
0.6667 Remote Similarity NPC8091
0.6667 Remote Similarity NPC472008
0.6628 Remote Similarity NPC166110
0.6628 Remote Similarity NPC476484
0.6625 Remote Similarity NPC475833
0.6625 Remote Similarity NPC149237
0.6625 Remote Similarity NPC225515
0.6625 Remote Similarity NPC478262
0.662 Remote Similarity NPC474329
0.662 Remote Similarity NPC474304
0.6588 Remote Similarity NPC280833
0.6585 Remote Similarity NPC474359
0.6582 Remote Similarity NPC27817
0.6575 Remote Similarity NPC477452
0.6571 Remote Similarity NPC32285
0.6571 Remote Similarity NPC288253
0.6557 Remote Similarity NPC100380
0.6552 Remote Similarity NPC248193
0.6548 Remote Similarity NPC471739
0.6543 Remote Similarity NPC471326
0.6543 Remote Similarity NPC221231
0.6538 Remote Similarity NPC316324
0.6538 Remote Similarity NPC471225
0.6538 Remote Similarity NPC472300
0.6533 Remote Similarity NPC84038
0.6533 Remote Similarity NPC186531
0.6533 Remote Similarity NPC84790
0.6533 Remote Similarity NPC66365
0.6515 Remote Similarity NPC223677
0.6515 Remote Similarity NPC28779
0.6515 Remote Similarity NPC200845
0.6515 Remote Similarity NPC128061
0.6515 Remote Similarity NPC10316
0.6515 Remote Similarity NPC228473
0.6515 Remote Similarity NPC275472
0.6512 Remote Similarity NPC471399
0.6508 Remote Similarity NPC474391
0.6508 Remote Similarity NPC224227
0.6508 Remote Similarity NPC228776
0.6508 Remote Similarity NPC176819
0.6508 Remote Similarity NPC163984
0.6508 Remote Similarity NPC58970
0.6506 Remote Similarity NPC2640
0.6506 Remote Similarity NPC475614
0.6506 Remote Similarity NPC96621
0.6506 Remote Similarity NPC90287
0.65 Remote Similarity NPC162741
0.65 Remote Similarity NPC91332
0.6494 Remote Similarity NPC175079
0.6494 Remote Similarity NPC329826
0.6494 Remote Similarity NPC193351
0.6494 Remote Similarity NPC138408
0.6494 Remote Similarity NPC244166
0.6494 Remote Similarity NPC114236
0.6494 Remote Similarity NPC155587
0.6494 Remote Similarity NPC226669
0.6494 Remote Similarity NPC469414
0.6486 Remote Similarity NPC199557
0.6486 Remote Similarity NPC261398
0.6479 Remote Similarity NPC212210
0.6479 Remote Similarity NPC477456
0.6479 Remote Similarity NPC477457
0.6471 Remote Similarity NPC311852
0.6471 Remote Similarity NPC241507
0.6463 Remote Similarity NPC105803
0.6463 Remote Similarity NPC477786
0.6463 Remote Similarity NPC477784
0.6463 Remote Similarity NPC474703
0.6463 Remote Similarity NPC477785
0.6462 Remote Similarity NPC296311
0.6462 Remote Similarity NPC268564
0.6462 Remote Similarity NPC474141
0.6462 Remote Similarity NPC71761

  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 NPC151728 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
0.9508 High Similarity NPD6108 Clinical (unspecified phase)
0.8413 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.8308 Intermediate Similarity NPD3704 Approved
0.8169 Intermediate Similarity NPD4756 Discovery
0.7903 Intermediate Similarity NPD8779 Phase 3
0.7 Intermediate Similarity NPD7331 Phase 2
0.6923 Remote Similarity NPD4695 Discontinued
0.6515 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6406 Remote Similarity NPD29 Approved
0.6406 Remote Similarity NPD28 Approved
0.6389 Remote Similarity NPD7341 Phase 2
0.6279 Remote Similarity NPD6672 Approved
0.6279 Remote Similarity NPD5737 Approved
0.625 Remote Similarity NPD3197 Phase 1
0.6212 Remote Similarity NPD3172 Approved
0.6119 Remote Similarity NPD3196 Approved
0.6119 Remote Similarity NPD4266 Approved
0.6119 Remote Similarity NPD3194 Approved
0.6119 Remote Similarity NPD3195 Phase 2
0.6111 Remote Similarity NPD5282 Discontinued
0.6098 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6071 Remote Similarity NPD6110 Phase 1
0.6049 Remote Similarity NPD3617 Approved
0.6047 Remote Similarity NPD5690 Phase 2
0.6047 Remote Similarity NPD5279 Phase 3
0.6023 Remote Similarity NPD6904 Approved
0.6023 Remote Similarity NPD6080 Approved
0.6023 Remote Similarity NPD6673 Approved
0.6 Remote Similarity NPD4197 Approved
0.5974 Remote Similarity NPD4691 Approved
0.5955 Remote Similarity NPD5692 Phase 3
0.593 Remote Similarity NPD1696 Phase 3
0.593 Remote Similarity NPD1694 Approved
0.593 Remote Similarity NPD5329 Approved
0.5902 Remote Similarity NPD9297 Discontinued
0.5902 Remote Similarity NPD9091 Suspended
0.5889 Remote Similarity NPD5693 Phase 1
0.5889 Remote Similarity NPD6050 Approved
0.5889 Remote Similarity NPD5694 Approved
0.5875 Remote Similarity NPD8039 Approved
0.5873 Remote Similarity NPD3174 Discontinued
0.587 Remote Similarity NPD5695 Phase 3
0.5862 Remote Similarity NPD7521 Approved
0.5862 Remote Similarity NPD5330 Approved
0.5862 Remote Similarity NPD7334 Approved
0.5862 Remote Similarity NPD6098 Approved
0.5862 Remote Similarity NPD5280 Approved
0.5862 Remote Similarity NPD6409 Approved
0.5862 Remote Similarity NPD7146 Approved
0.5862 Remote Similarity NPD6684 Approved
0.5862 Remote Similarity NPD4694 Approved
0.5844 Remote Similarity NPD4137 Phase 3
0.5843 Remote Similarity NPD4753 Phase 2
0.5843 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5814 Remote Similarity NPD3665 Phase 1
0.5814 Remote Similarity NPD3133 Approved
0.5814 Remote Similarity NPD3666 Approved
0.5795 Remote Similarity NPD3573 Approved
0.5775 Remote Similarity NPD287 Approved
0.5769 Remote Similarity NPD4747 Approved
0.5765 Remote Similarity NPD4221 Approved
0.5765 Remote Similarity NPD3667 Approved
0.5765 Remote Similarity NPD4223 Phase 3
0.5765 Remote Similarity NPD4752 Clinical (unspecified phase)
0.575 Remote Similarity NPD4058 Approved
0.5745 Remote Similarity NPD6084 Phase 2
0.5745 Remote Similarity NPD6083 Phase 2
0.573 Remote Similarity NPD6903 Approved
0.573 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5699 Remote Similarity NPD4629 Approved
0.5699 Remote Similarity NPD5210 Approved
0.5698 Remote Similarity NPD7154 Phase 3
0.5696 Remote Similarity NPD5276 Approved
0.5692 Remote Similarity NPD622 Approved
0.5684 Remote Similarity NPD5696 Approved
0.5682 Remote Similarity NPD3618 Phase 1
0.5667 Remote Similarity NPD5783 Phase 3
0.5638 Remote Similarity NPD5221 Approved
0.5638 Remote Similarity NPD5222 Approved
0.5638 Remote Similarity NPD5220 Clinical (unspecified phase)
0.5632 Remote Similarity NPD3668 Phase 3
0.5632 Remote Similarity NPD4786 Approved
0.5625 Remote Similarity NPD9090 Phase 3
0.5606 Remote Similarity NPD3173 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