Structure

Physi-Chem Properties

Molecular Weight:  210.09
Volume:  214.871
LogP:  0.813
LogD:  0.696
LogS:  -0.927
# Rotatable Bonds:  3
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.743
Synthetic Accessibility Score:  2.464
Fsp3:  0.364
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.677
MDCK Permeability:  1.2831370440835599e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.844
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.869
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  75.37793731689453%
Volume Distribution (VD):  0.562
Pgp-substrate:  12.952962875366211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.267
CYP1A2-substrate:  0.933
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.7
CYP2C9-inhibitor:  0.078
CYP2C9-substrate:  0.863
CYP2D6-inhibitor:  0.055
CYP2D6-substrate:  0.706
CYP3A4-inhibitor:  0.034
CYP3A4-substrate:  0.389

ADMET: Excretion

Clearance (CL):  16.083
Half-life (T1/2):  0.918

ADMET: Toxicity

hERG Blockers:  0.054
Human Hepatotoxicity (H-HT):  0.25
Drug-inuced Liver Injury (DILI):  0.398
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.18
Maximum Recommended Daily Dose:  0.212
Skin Sensitization:  0.855
Carcinogencity:  0.031
Eye Corrosion:  0.146
Eye Irritation:  0.918
Respiratory Toxicity:  0.118

Download Data

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

  Natural Product: NPC251429

Natural Product ID:  NPC251429
Common Name*:   Anserinone B
IUPAC Name:   3-[(2S)-2-hydroxypropyl]-5-methoxy-2-methylcyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  UDHYZSNFKHIRSC-LURJTMIESA-N
Standard InCHI:  InChI=1S/C11H14O4/c1-6(12)4-8-7(2)9(13)5-10(15-3)11(8)14/h5-6,12H,4H2,1-3H3/t6-/m0/s1
SMILES:  C[C@@H](CC1=C(C)C(=O)C=C(C1=O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL510286
PubChem CID:   177382
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. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea 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 = 700.0 Zone units PMID[529370]
NPT730 Cell Line MC-38 Mus musculus Activity = 400.0 Zone units PMID[529370]
NPT404 Cell Line CCRF-CEM Homo sapiens Activity = 650.0 Zone units PMID[529370]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 = 3.6 ug.mL-1 PMID[529370]
NPT3095 Organism Sordaria fimicola Sordaria fimicola Activity = 50.0 % PMID[529369]
NPT3096 Organism Ascobolus Ascobolus Activity = 37.0 % PMID[529369]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 40.0 mm PMID[529369]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 40.0 mm PMID[529369]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 21000.0 nM PMID[529369]
NPT27 Others Unspecified Activity = 650.0 Zone units PMID[529370]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 400.0 Zone units PMID[529370]

☑ 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 NPC251429 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
0.8788 High Similarity NPC298249
0.8125 Intermediate Similarity NPC139056
0.8 Intermediate Similarity NPC94488
0.7971 Intermediate Similarity NPC243272
0.7857 Intermediate Similarity NPC263382
0.7857 Intermediate Similarity NPC146376
0.7857 Intermediate Similarity NPC125578
0.7846 Intermediate Similarity NPC320421
0.7746 Intermediate Similarity NPC262673
0.7742 Intermediate Similarity NPC137396
0.7733 Intermediate Similarity NPC473536
0.7727 Intermediate Similarity NPC473494
0.7639 Intermediate Similarity NPC107848
0.7639 Intermediate Similarity NPC291062
0.7639 Intermediate Similarity NPC94743
0.7619 Intermediate Similarity NPC474805
0.75 Intermediate Similarity NPC317796
0.75 Intermediate Similarity NPC469884
0.7391 Intermediate Similarity NPC143168
0.7391 Intermediate Similarity NPC57463
0.7391 Intermediate Similarity NPC151728
0.7391 Intermediate Similarity NPC53109
0.7333 Intermediate Similarity NPC264178
0.7302 Intermediate Similarity NPC22329
0.7286 Intermediate Similarity NPC474400
0.7286 Intermediate Similarity NPC34622
0.7286 Intermediate Similarity NPC7029
0.7284 Intermediate Similarity NPC469809
0.725 Intermediate Similarity NPC47450
0.7246 Intermediate Similarity NPC68044
0.7222 Intermediate Similarity NPC474619
0.7183 Intermediate Similarity NPC98897
0.7164 Intermediate Similarity NPC224103
0.7164 Intermediate Similarity NPC200831
0.7164 Intermediate Similarity NPC299369
0.7143 Intermediate Similarity NPC477830
0.7143 Intermediate Similarity NPC477708
0.7143 Intermediate Similarity NPC220191
0.7125 Intermediate Similarity NPC221510
0.7125 Intermediate Similarity NPC159714
0.7123 Intermediate Similarity NPC134385
0.7083 Intermediate Similarity NPC472072
0.7083 Intermediate Similarity NPC16119
0.7073 Intermediate Similarity NPC474251
0.7051 Intermediate Similarity NPC272267
0.6988 Remote Similarity NPC77971
0.6962 Remote Similarity NPC264391
0.6897 Remote Similarity NPC146852
0.6883 Remote Similarity NPC147438
0.6875 Remote Similarity NPC291260
0.6849 Remote Similarity NPC137163
0.6835 Remote Similarity NPC471061
0.6829 Remote Similarity NPC253364
0.6818 Remote Similarity NPC61275
0.6786 Remote Similarity NPC471223
0.6786 Remote Similarity NPC67081
0.6782 Remote Similarity NPC274075
0.6761 Remote Similarity NPC269737
0.6757 Remote Similarity NPC106613
0.6716 Remote Similarity NPC129710
0.6709 Remote Similarity NPC26504
0.6707 Remote Similarity NPC67254
0.6667 Remote Similarity NPC268185
0.6667 Remote Similarity NPC219966
0.6667 Remote Similarity NPC474774
0.663 Remote Similarity NPC300584
0.6625 Remote Similarity NPC82666
0.6625 Remote Similarity NPC97173
0.6622 Remote Similarity NPC469446
0.6615 Remote Similarity NPC225974
0.6613 Remote Similarity NPC106547
0.6585 Remote Similarity NPC91332
0.6585 Remote Similarity NPC162741
0.6567 Remote Similarity NPC168521
0.6552 Remote Similarity NPC53454
0.6543 Remote Similarity NPC231739
0.6543 Remote Similarity NPC478122
0.6533 Remote Similarity NPC269985
0.6533 Remote Similarity NPC122627
0.6522 Remote Similarity NPC20066
0.6508 Remote Similarity NPC110396
0.6506 Remote Similarity NPC280367
0.65 Remote Similarity NPC16279
0.65 Remote Similarity NPC205615
0.65 Remote Similarity NPC256640
0.65 Remote Similarity NPC271986
0.6494 Remote Similarity NPC202011
0.6494 Remote Similarity NPC318766
0.6494 Remote Similarity NPC173321
0.6486 Remote Similarity NPC101670
0.6479 Remote Similarity NPC38455
0.6463 Remote Similarity NPC475681
0.6447 Remote Similarity NPC287705
0.6447 Remote Similarity NPC238223
0.6444 Remote Similarity NPC327620
0.6437 Remote Similarity NPC142583
0.6437 Remote Similarity NPC472007
0.6437 Remote Similarity NPC300779
0.6429 Remote Similarity NPC38796
0.6429 Remote Similarity NPC158411
0.642 Remote Similarity NPC475711
0.642 Remote Similarity NPC47844
0.642 Remote Similarity NPC141195
0.641 Remote Similarity NPC474539
0.6404 Remote Similarity NPC471399
0.64 Remote Similarity NPC83965
0.6395 Remote Similarity NPC263997
0.6395 Remote Similarity NPC132228
0.6395 Remote Similarity NPC241512
0.6395 Remote Similarity NPC32037
0.6395 Remote Similarity NPC6185
0.6395 Remote Similarity NPC8518
0.6395 Remote Similarity NPC242233
0.6395 Remote Similarity NPC187529
0.6375 Remote Similarity NPC478195
0.6375 Remote Similarity NPC478196
0.6375 Remote Similarity NPC478192
0.6375 Remote Similarity NPC478194
0.6375 Remote Similarity NPC478193
0.6375 Remote Similarity NPC478191
0.6364 Remote Similarity NPC119740
0.6364 Remote Similarity NPC107703
0.6364 Remote Similarity NPC288381
0.6364 Remote Similarity NPC150063
0.6364 Remote Similarity NPC475982
0.6364 Remote Similarity NPC20934
0.6354 Remote Similarity NPC320294
0.6353 Remote Similarity NPC477784
0.6353 Remote Similarity NPC477785
0.6353 Remote Similarity NPC477786
0.6338 Remote Similarity NPC281195
0.6333 Remote Similarity NPC303230
0.6333 Remote Similarity NPC6099
0.6333 Remote Similarity NPC32552
0.6333 Remote Similarity NPC327760
0.6333 Remote Similarity NPC114345
0.6324 Remote Similarity NPC217188
0.6322 Remote Similarity NPC186332
0.6322 Remote Similarity NPC203795
0.6322 Remote Similarity NPC47937
0.6322 Remote Similarity NPC47220
0.6322 Remote Similarity NPC472009
0.6316 Remote Similarity NPC132286
0.6316 Remote Similarity NPC203335
0.631 Remote Similarity NPC474980
0.6301 Remote Similarity NPC260573
0.6292 Remote Similarity NPC87306
0.6282 Remote Similarity NPC477455
0.6277 Remote Similarity NPC475284
0.6277 Remote Similarity NPC281608
0.6265 Remote Similarity NPC19900
0.625 Remote Similarity NPC473248
0.625 Remote Similarity NPC474545
0.625 Remote Similarity NPC197835
0.625 Remote Similarity NPC189609
0.625 Remote Similarity NPC140591
0.625 Remote Similarity NPC303653
0.625 Remote Similarity NPC160540
0.625 Remote Similarity NPC291500
0.625 Remote Similarity NPC114727
0.625 Remote Similarity NPC158853
0.625 Remote Similarity NPC476590
0.6237 Remote Similarity NPC279722
0.6235 Remote Similarity NPC103486
0.6234 Remote Similarity NPC309466
0.6234 Remote Similarity NPC477452
0.6222 Remote Similarity NPC473455
0.6222 Remote Similarity NPC265856
0.6222 Remote Similarity NPC131864
0.6222 Remote Similarity NPC474209
0.6222 Remote Similarity NPC475823
0.6222 Remote Similarity NPC166554
0.622 Remote Similarity NPC211279
0.6216 Remote Similarity NPC477707
0.6207 Remote Similarity NPC182383
0.6207 Remote Similarity NPC90287
0.6207 Remote Similarity NPC470177
0.6203 Remote Similarity NPC133098
0.6197 Remote Similarity NPC192843
0.6197 Remote Similarity NPC71755
0.6196 Remote Similarity NPC217624
0.6196 Remote Similarity NPC181393
0.619 Remote Similarity NPC470945
0.619 Remote Similarity NPC470947
0.619 Remote Similarity NPC470946
0.619 Remote Similarity NPC74086
0.6184 Remote Similarity NPC475675
0.6184 Remote Similarity NPC475555
0.618 Remote Similarity NPC471755
0.618 Remote Similarity NPC476708
0.618 Remote Similarity NPC471756
0.618 Remote Similarity NPC472008
0.6173 Remote Similarity NPC474885
0.6163 Remote Similarity NPC62214
0.6163 Remote Similarity NPC116543
0.6154 Remote Similarity NPC250928
0.6154 Remote Similarity NPC236208
0.6154 Remote Similarity NPC474060
0.6154 Remote Similarity NPC10758
0.6145 Remote Similarity NPC321180

  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 NPC251429 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
0.7826 Intermediate Similarity NPD3704 Approved
0.7595 Intermediate Similarity NPD6110 Phase 1
0.7391 Intermediate Similarity NPD2664 Clinical (unspecified phase)
0.7164 Intermediate Similarity NPD8779 Phase 3
0.7083 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.7051 Intermediate Similarity NPD4756 Discovery
0.6374 Remote Similarity NPD5282 Discontinued
0.625 Remote Similarity NPD9090 Phase 3
0.619 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6 Remote Similarity NPD4695 Discontinued
0.5946 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5915 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5897 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5843 Remote Similarity NPD1696 Phase 3
0.5781 Remote Similarity NPD9297 Discontinued
0.5781 Remote Similarity NPD9091 Suspended
0.5769 Remote Similarity NPD7331 Phase 2
0.5714 Remote Similarity NPD3197 Phase 1
0.5699 Remote Similarity NPD6698 Approved
0.5699 Remote Similarity NPD46 Approved
0.5676 Remote Similarity NPD6109 Phase 1
0.5604 Remote Similarity NPD4249 Approved
0.5604 Remote Similarity NPD5279 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