Structure

Physi-Chem Properties

Molecular Weight:  578.14
Volume:  555.862
LogP:  3.982
LogD:  2.356
LogS:  -4.387
# Rotatable Bonds:  7
TPSA:  196.35
# H-Bond Aceptor:  12
# H-Bond Donor:  6
# Rings:  5
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.145
Synthetic Accessibility Score:  4.185
Fsp3:  0.2
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.265
MDCK Permeability:  1.7497239241492935e-05
Pgp-inhibitor:  0.039
Pgp-substrate:  0.847
Human Intestinal Absorption (HIA):  0.102
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  100.78555297851562%
Volume Distribution (VD):  0.594
Pgp-substrate:  1.6671881675720215%

ADMET: Metabolism

CYP1A2-inhibitor:  0.617
CYP1A2-substrate:  0.039
CYP2C19-inhibitor:  0.411
CYP2C19-substrate:  0.049
CYP2C9-inhibitor:  0.625
CYP2C9-substrate:  0.885
CYP2D6-inhibitor:  0.733
CYP2D6-substrate:  0.21
CYP3A4-inhibitor:  0.446
CYP3A4-substrate:  0.062

ADMET: Excretion

Clearance (CL):  4.282
Half-life (T1/2):  0.784

ADMET: Toxicity

hERG Blockers:  0.145
Human Hepatotoxicity (H-HT):  0.612
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.766
Rat Oral Acute Toxicity:  0.042
Maximum Recommended Daily Dose:  0.041
Skin Sensitization:  0.927
Carcinogencity:  0.142
Eye Corrosion:  0.003
Eye Irritation:  0.18
Respiratory Toxicity:  0.038

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC139056

Natural Product ID:  NPC139056
Common Name*:   Anserinone A
IUPAC Name:   5-methoxy-2-methyl-3-(2-oxopropyl)cyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  MIKCTUJVVLWHFM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H12O4/c1-6(12)4-8-7(2)9(13)5-10(15-3)11(8)14/h5H,4H2,1-3H3
SMILES:  COC1=CC(=O)C(=C(C1=O)CC(=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL504895
PubChem CID:   177381
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
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10479323]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12350167]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[14640527]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota Axinella verrucosa Mediterranean n.a. PMID[14738391]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15043411]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Sussex Inlet, New South Wales, Australia n.a. PMID[15104517]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15332862]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Berkeley Pit lake n.a. PMID[17970594]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. New Zealand n.a. PMID[19323568]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19326880]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20452770]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Limonium tubiflorum n.a. PMID[21146414]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21916432]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22148349]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22458669]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23360521]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23477451]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23603293]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23972215]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24033077]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24437979]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31433188]
NPO20654 Podospora anserina Species Lasiosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[9214737]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[9392888]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO20654 Podospora anserina Species Lasiosphaeriaceae 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
NPT137 Cell Line L1210 Mus musculus Activity = 300.0 Zone units PMID[469665]
NPT730 Cell Line MC-38 Mus musculus Activity = 300.0 Zone units PMID[469665]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 = 2.22 ug.mL-1 PMID[469665]
NPT3095 Organism Sordaria fimicola Sordaria fimicola Activity = 60.0 % PMID[469664]
NPT3096 Organism Ascobolus Ascobolus Activity = 100.0 % PMID[469664]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 40.0 mm PMID[469664]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 40.0 mm PMID[469664]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 9100.0 nM PMID[469664]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 50.0 Zone units PMID[469665]
NPT27 Others Unspecified Activity = 150.0 Zone units PMID[469665]

☑ 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 NPC139056 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
0.8793 High Similarity NPC473494
0.8727 High Similarity NPC474805
0.8571 High Similarity NPC317796
0.8364 Intermediate Similarity NPC22329
0.8361 Intermediate Similarity NPC57463
0.8361 Intermediate Similarity NPC151728
0.8226 Intermediate Similarity NPC474400
0.8226 Intermediate Similarity NPC34622
0.8182 Intermediate Similarity NPC220191
0.8136 Intermediate Similarity NPC299369
0.8136 Intermediate Similarity NPC200831
0.8136 Intermediate Similarity NPC224103
0.8125 Intermediate Similarity NPC298249
0.8125 Intermediate Similarity NPC251429
0.8125 Intermediate Similarity NPC243272
0.8125 Intermediate Similarity NPC474619
0.8095 Intermediate Similarity NPC98897
0.8 Intermediate Similarity NPC134385
0.8 Intermediate Similarity NPC320421
0.8 Intermediate Similarity NPC146376
0.8 Intermediate Similarity NPC125578
0.8 Intermediate Similarity NPC263382
0.7969 Intermediate Similarity NPC16119
0.7895 Intermediate Similarity NPC137396
0.7879 Intermediate Similarity NPC94488
0.7879 Intermediate Similarity NPC262673
0.7761 Intermediate Similarity NPC94743
0.7761 Intermediate Similarity NPC291062
0.7627 Intermediate Similarity NPC129710
0.7593 Intermediate Similarity NPC106547
0.75 Intermediate Similarity NPC143168
0.75 Intermediate Similarity NPC53109
0.7458 Intermediate Similarity NPC168521
0.7455 Intermediate Similarity NPC110396
0.7429 Intermediate Similarity NPC264178
0.7385 Intermediate Similarity NPC7029
0.7231 Intermediate Similarity NPC477830
0.7143 Intermediate Similarity NPC474539
0.7123 Intermediate Similarity NPC473536
0.6944 Remote Similarity NPC147438
0.6923 Remote Similarity NPC469884
0.6842 Remote Similarity NPC191337
0.6835 Remote Similarity NPC2640
0.6835 Remote Similarity NPC475614
0.6818 Remote Similarity NPC68044
0.6757 Remote Similarity NPC26504
0.6716 Remote Similarity NPC474774
0.6667 Remote Similarity NPC477686
0.6667 Remote Similarity NPC283087
0.6667 Remote Similarity NPC25771
0.6667 Remote Similarity NPC15325
0.6667 Remote Similarity NPC133098
0.6571 Remote Similarity NPC203335
0.6552 Remote Similarity NPC166788
0.6545 Remote Similarity NPC111474
0.6538 Remote Similarity NPC474085
0.6533 Remote Similarity NPC477708
0.6491 Remote Similarity NPC292463
0.6479 Remote Similarity NPC134593
0.6471 Remote Similarity NPC477707
0.6456 Remote Similarity NPC47450
0.6441 Remote Similarity NPC471752
0.642 Remote Similarity NPC8518
0.642 Remote Similarity NPC263997
0.642 Remote Similarity NPC6185
0.642 Remote Similarity NPC241512
0.642 Remote Similarity NPC77971
0.642 Remote Similarity NPC132228
0.6418 Remote Similarity NPC79756
0.6393 Remote Similarity NPC176819
0.6393 Remote Similarity NPC163984
0.6393 Remote Similarity NPC228776
0.6393 Remote Similarity NPC58970
0.6364 Remote Similarity NPC281195
0.6329 Remote Similarity NPC474353
0.6301 Remote Similarity NPC107848
0.6286 Remote Similarity NPC101670
0.6269 Remote Similarity NPC203233
0.6267 Remote Similarity NPC122244
0.625 Remote Similarity NPC113082
0.6235 Remote Similarity NPC223093
0.6234 Remote Similarity NPC471225
0.6234 Remote Similarity NPC272267
0.622 Remote Similarity NPC133652
0.622 Remote Similarity NPC470177
0.6216 Remote Similarity NPC66365
0.6212 Remote Similarity NPC192843
0.6212 Remote Similarity NPC268185
0.6197 Remote Similarity NPC472072
0.6197 Remote Similarity NPC469446
0.6197 Remote Similarity NPC248125
0.6197 Remote Similarity NPC137163
0.6173 Remote Similarity NPC288281
0.6173 Remote Similarity NPC8091
0.6164 Remote Similarity NPC474060
0.6154 Remote Similarity NPC248624
0.6154 Remote Similarity NPC23778
0.6129 Remote Similarity NPC32351
0.6129 Remote Similarity NPC118788
0.6125 Remote Similarity NPC286229
0.6125 Remote Similarity NPC99308
0.6104 Remote Similarity NPC271986
0.6102 Remote Similarity NPC471753
0.6098 Remote Similarity NPC469809
0.6094 Remote Similarity NPC37644
0.6087 Remote Similarity NPC151648
0.6076 Remote Similarity NPC475681
0.6076 Remote Similarity NPC291260
0.6076 Remote Similarity NPC471740
0.6066 Remote Similarity NPC324812
0.6047 Remote Similarity NPC475823
0.6047 Remote Similarity NPC474209
0.6032 Remote Similarity NPC64866
0.6029 Remote Similarity NPC38455
0.6029 Remote Similarity NPC133600
0.6024 Remote Similarity NPC474680
0.6024 Remote Similarity NPC281172
0.6 Remote Similarity NPC150063
0.6 Remote Similarity NPC53454
0.6 Remote Similarity NPC119740
0.6 Remote Similarity NPC162741
0.6 Remote Similarity NPC158853
0.6 Remote Similarity NPC472008
0.6 Remote Similarity NPC474658
0.6 Remote Similarity NPC91332
0.5977 Remote Similarity NPC32944
0.5977 Remote Similarity NPC193396
0.5972 Remote Similarity NPC83965
0.597 Remote Similarity NPC283502
0.597 Remote Similarity NPC281230
0.5968 Remote Similarity NPC145311
0.5952 Remote Similarity NPC203795
0.5952 Remote Similarity NPC291712
0.5952 Remote Similarity NPC472009
0.5949 Remote Similarity NPC478246
0.5949 Remote Similarity NPC478247
0.5949 Remote Similarity NPC264391
0.5949 Remote Similarity NPC478122
0.5946 Remote Similarity NPC476059
0.5946 Remote Similarity NPC473603
0.5946 Remote Similarity NPC469914
0.5942 Remote Similarity NPC429928
0.5942 Remote Similarity NPC229252
0.5942 Remote Similarity NPC309408
0.5942 Remote Similarity NPC143857
0.5938 Remote Similarity NPC471751
0.5938 Remote Similarity NPC216407
0.5932 Remote Similarity NPC301972
0.593 Remote Similarity NPC95364
0.593 Remote Similarity NPC280833
0.593 Remote Similarity NPC142159
0.5926 Remote Similarity NPC475833
0.5926 Remote Similarity NPC221510
0.5926 Remote Similarity NPC275766
0.5926 Remote Similarity NPC275507
0.5926 Remote Similarity NPC159714
0.5926 Remote Similarity NPC55869
0.5915 Remote Similarity NPC475618
0.5909 Remote Similarity NPC25038
0.5909 Remote Similarity NPC297280
0.5904 Remote Similarity NPC474251
0.5902 Remote Similarity NPC8610
0.5902 Remote Similarity NPC100380
0.5902 Remote Similarity NPC262558
0.5897 Remote Similarity NPC205615
0.5897 Remote Similarity NPC16279
0.5897 Remote Similarity NPC110725
0.5897 Remote Similarity NPC256640
0.589 Remote Similarity NPC122627
0.589 Remote Similarity NPC473213
0.589 Remote Similarity NPC132286
0.589 Remote Similarity NPC106613
0.5889 Remote Similarity NPC318082
0.5882 Remote Similarity NPC311852
0.5882 Remote Similarity NPC472007
0.5882 Remote Similarity NPC300779
0.5882 Remote Similarity NPC471739
0.5873 Remote Similarity NPC107703
0.5873 Remote Similarity NPC225974
0.5867 Remote Similarity NPC477455
0.5867 Remote Similarity NPC318766
0.5867 Remote Similarity NPC173321
0.5862 Remote Similarity NPC224270
0.5862 Remote Similarity NPC471399
0.5857 Remote Similarity NPC15193
0.5857 Remote Similarity NPC269737
0.5854 Remote Similarity NPC103486
0.5854 Remote Similarity NPC221231
0.5854 Remote Similarity NPC471326
0.5846 Remote Similarity NPC296311
0.5846 Remote Similarity NPC268564
0.5844 Remote Similarity NPC259599
0.5844 Remote Similarity NPC294434
0.5844 Remote Similarity NPC160540
0.5844 Remote Similarity NPC117746
0.5844 Remote Similarity NPC15499
0.5844 Remote Similarity NPC215050
0.5833 Remote Similarity NPC90287
0.5833 Remote Similarity NPC32037
0.5823 Remote Similarity NPC97173

  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 NPC139056 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
0.8136 Intermediate Similarity NPD8779 Phase 3
0.7969 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7424 Intermediate Similarity NPD3704 Approved
0.7123 Intermediate Similarity NPD4756 Discovery
0.6375 Remote Similarity NPD6110 Phase 1
0.6316 Remote Similarity NPD9297 Discontinued
0.6316 Remote Similarity NPD9091 Suspended
0.6 Remote Similarity NPD4695 Discontinued
0.6 Remote Similarity NPD9090 Phase 3
0.5972 Remote Similarity NPD7331 Phase 2
0.5672 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5647 Remote Similarity NPD1696 Phase 3
0.5616 Remote Similarity NPD7341 Phase 2
0.561 Remote Similarity NPD8259 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