Structure

Physi-Chem Properties

Molecular Weight:  238.08
Volume:  238.321
LogP:  1.555
LogD:  1.598
LogS:  -3.035
# Rotatable Bonds:  4
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  3.208
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.407
MDCK Permeability:  3.011584522027988e-05
Pgp-inhibitor:  0.755
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.984
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.057
Plasma Protein Binding (PPB):  89.1186294555664%
Volume Distribution (VD):  0.72
Pgp-substrate:  6.849960803985596%

ADMET: Metabolism

CYP1A2-inhibitor:  0.991
CYP1A2-substrate:  0.934
CYP2C19-inhibitor:  0.962
CYP2C19-substrate:  0.738
CYP2C9-inhibitor:  0.602
CYP2C9-substrate:  0.195
CYP2D6-inhibitor:  0.96
CYP2D6-substrate:  0.017
CYP3A4-inhibitor:  0.858
CYP3A4-substrate:  0.164

ADMET: Excretion

Clearance (CL):  4.979
Half-life (T1/2):  0.607

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.723
Drug-inuced Liver Injury (DILI):  0.691
AMES Toxicity:  0.136
Rat Oral Acute Toxicity:  0.864
Maximum Recommended Daily Dose:  0.276
Skin Sensitization:  0.899
Carcinogencity:  0.079
Eye Corrosion:  0.036
Eye Irritation:  0.876
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC129710

Natural Product ID:  NPC129710
Common Name*:   2,3,5-Trimethoxy-6-(1-Propenyl)-2,5-Cyclohexadiene-1,4-Dione
IUPAC Name:   2,3,5-trimethoxy-6-[(E)-prop-1-enyl]cyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  RTBKABKNDSZTIA-AATRIKPKSA-N
Standard InCHI:  InChI=1S/C12H14O5/c1-5-6-7-8(13)11(16-3)12(17-4)9(14)10(7)15-2/h5-6H,1-4H3/b6-5+
SMILES:  C/C=C/C1=C(C(=O)C(=C(C1=O)OC)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL454996
PubChem CID:   10868332
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001534] Quinone and hydroquinone lipids
          • [CHEMONTID:0002802] Prenylquinones
            • [CHEMONTID:0001545] Ubiquinones

*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
NPO6580 Smirnowia iranica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12502308]
NPO6580 Smirnowia iranica Species Fabaceae 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 256000.0 nM PMID[510317]
NPT841 Organism Leishmania major Leishmania major IC50 = 72000.0 nM PMID[510317]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 = 74000.0 nM PMID[510317]
NPT633 Organism Leishmania donovani Leishmania donovani IC50 = 97000.0 nM PMID[510317]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 200000.0 nM PMID[510317]
NPT633 Organism Leishmania donovani Leishmania donovani IC50 > 800000.0 nM PMID[510317]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 > 800000.0 nM PMID[510317]

☑ 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 NPC129710 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
0.902 High Similarity NPC22329
0.8824 High Similarity NPC220191
0.8519 High Similarity NPC317796
0.8333 Intermediate Similarity NPC474805
0.807 Intermediate Similarity NPC299369
0.807 Intermediate Similarity NPC224103
0.807 Intermediate Similarity NPC200831
0.8039 Intermediate Similarity NPC110396
0.7843 Intermediate Similarity NPC106547
0.7679 Intermediate Similarity NPC168521
0.7627 Intermediate Similarity NPC139056
0.75 Intermediate Similarity NPC473494
0.7231 Intermediate Similarity NPC474619
0.7193 Intermediate Similarity NPC137396
0.7167 Intermediate Similarity NPC474825
0.7143 Intermediate Similarity NPC57463
0.7143 Intermediate Similarity NPC151728
0.7119 Intermediate Similarity NPC25038
0.7077 Intermediate Similarity NPC16119
0.7059 Intermediate Similarity NPC111474
0.7031 Intermediate Similarity NPC474400
0.7031 Intermediate Similarity NPC475618
0.7031 Intermediate Similarity NPC34622
0.7015 Intermediate Similarity NPC262673
0.7 Intermediate Similarity NPC150717
0.7 Intermediate Similarity NPC221763
0.6935 Remote Similarity NPC133600
0.6923 Remote Similarity NPC98897
0.6912 Remote Similarity NPC291062
0.6912 Remote Similarity NPC94743
0.6897 Remote Similarity NPC46565
0.6897 Remote Similarity NPC229046
0.6825 Remote Similarity NPC309408
0.6774 Remote Similarity NPC281195
0.6719 Remote Similarity NPC68044
0.6716 Remote Similarity NPC243272
0.6716 Remote Similarity NPC251429
0.6716 Remote Similarity NPC298249
0.6667 Remote Similarity NPC203233
0.6667 Remote Similarity NPC7940
0.662 Remote Similarity NPC264178
0.6618 Remote Similarity NPC134385
0.6618 Remote Similarity NPC134593
0.6618 Remote Similarity NPC125578
0.6618 Remote Similarity NPC146376
0.6618 Remote Similarity NPC263382
0.6571 Remote Similarity NPC474539
0.6552 Remote Similarity NPC107703
0.6545 Remote Similarity NPC477686
0.6522 Remote Similarity NPC94488
0.6508 Remote Similarity NPC320421
0.6462 Remote Similarity NPC15193
0.6429 Remote Similarity NPC158853
0.6429 Remote Similarity NPC191337
0.6429 Remote Similarity NPC166788
0.6418 Remote Similarity NPC476589
0.6393 Remote Similarity NPC478120
0.6389 Remote Similarity NPC147438
0.6377 Remote Similarity NPC477117
0.6338 Remote Similarity NPC66365
0.6333 Remote Similarity NPC191643
0.6324 Remote Similarity NPC469446
0.629 Remote Similarity NPC173157
0.629 Remote Similarity NPC297280
0.6282 Remote Similarity NPC288281
0.6271 Remote Similarity NPC118788
0.6271 Remote Similarity NPC15325
0.625 Remote Similarity NPC25771
0.625 Remote Similarity NPC189700
0.623 Remote Similarity NPC37644
0.6216 Remote Similarity NPC26504
0.62 Remote Similarity NPC12889
0.6176 Remote Similarity NPC101670
0.6176 Remote Similarity NPC471566
0.6176 Remote Similarity NPC182794
0.6176 Remote Similarity NPC471565
0.6167 Remote Similarity NPC30433
0.6154 Remote Similarity NPC86789
0.6133 Remote Similarity NPC97173
0.6133 Remote Similarity NPC283087
0.6133 Remote Similarity NPC82666
0.6133 Remote Similarity NPC473536
0.6129 Remote Similarity NPC218486
0.6125 Remote Similarity NPC281172
0.6119 Remote Similarity NPC53109
0.6119 Remote Similarity NPC477830
0.6119 Remote Similarity NPC143168
0.6111 Remote Similarity NPC133098
0.6102 Remote Similarity NPC234084
0.6102 Remote Similarity NPC313553
0.6087 Remote Similarity NPC470033
0.6087 Remote Similarity NPC475555
0.6087 Remote Similarity NPC475675
0.6078 Remote Similarity NPC269641
0.6071 Remote Similarity NPC292463
0.6071 Remote Similarity NPC216921
0.6061 Remote Similarity NPC79756
0.6061 Remote Similarity NPC98519
0.6061 Remote Similarity NPC130953
0.6056 Remote Similarity NPC474060
0.6049 Remote Similarity NPC291712
0.6029 Remote Similarity NPC7029
0.6029 Remote Similarity NPC477457
0.6029 Remote Similarity NPC477456
0.6027 Remote Similarity NPC316851
0.6 Remote Similarity NPC266979
0.6 Remote Similarity NPC225974
0.6 Remote Similarity NPC132286
0.5972 Remote Similarity NPC59558
0.597 Remote Similarity NPC263732
0.5965 Remote Similarity NPC471753
0.5965 Remote Similarity NPC75134
0.5962 Remote Similarity NPC38497
0.5946 Remote Similarity NPC122244
0.5942 Remote Similarity NPC471556
0.5938 Remote Similarity NPC86948
0.5938 Remote Similarity NPC51846
0.5921 Remote Similarity NPC471225
0.5915 Remote Similarity NPC280374
0.5915 Remote Similarity NPC238223
0.5915 Remote Similarity NPC309466
0.5909 Remote Similarity NPC38455
0.5882 Remote Similarity NPC132243
0.5882 Remote Similarity NPC474774
0.5882 Remote Similarity NPC2328
0.5882 Remote Similarity NPC32552
0.5882 Remote Similarity NPC473737
0.5873 Remote Similarity NPC300121
0.5867 Remote Similarity NPC315552
0.5857 Remote Similarity NPC37382
0.5849 Remote Similarity NPC185839
0.5846 Remote Similarity NPC268185
0.5846 Remote Similarity NPC71755
0.5844 Remote Similarity NPC99182
0.5844 Remote Similarity NPC469510
0.5844 Remote Similarity NPC248624
0.5833 Remote Similarity NPC470693
0.5833 Remote Similarity NPC476059
0.5833 Remote Similarity NPC473603
0.5823 Remote Similarity NPC99308
0.5823 Remote Similarity NPC312419
0.5821 Remote Similarity NPC429928
0.5818 Remote Similarity NPC323278
0.5818 Remote Similarity NPC113082
0.5818 Remote Similarity NPC101147
0.5802 Remote Similarity NPC469884
0.5789 Remote Similarity NPC477708
0.5789 Remote Similarity NPC301972
0.5781 Remote Similarity NPC478117
0.5775 Remote Similarity NPC203335
0.5775 Remote Similarity NPC122627
0.5769 Remote Similarity NPC291260
0.5765 Remote Similarity NPC224270
0.5763 Remote Similarity NPC100380
0.5763 Remote Similarity NPC471752
0.5763 Remote Similarity NPC8610
0.5763 Remote Similarity NPC262558
0.5753 Remote Similarity NPC107848
0.5753 Remote Similarity NPC315285
0.5741 Remote Similarity NPC180840
0.5738 Remote Similarity NPC288381
0.5738 Remote Similarity NPC221467
0.5738 Remote Similarity NPC15789
0.5738 Remote Similarity NPC176819
0.5738 Remote Similarity NPC20934
0.5738 Remote Similarity NPC163984
0.5738 Remote Similarity NPC58970
0.5738 Remote Similarity NPC228776
0.5738 Remote Similarity NPC32351
0.5732 Remote Similarity NPC130030
0.5732 Remote Similarity NPC475614
0.5732 Remote Similarity NPC2640
0.5714 Remote Similarity NPC69898
0.5714 Remote Similarity NPC220766
0.5714 Remote Similarity NPC473825
0.5714 Remote Similarity NPC45283
0.5714 Remote Similarity NPC131174
0.5714 Remote Similarity NPC295777
0.5714 Remote Similarity NPC116366
0.5714 Remote Similarity NPC133904
0.5698 Remote Similarity NPC193396
0.5698 Remote Similarity NPC32944
0.5696 Remote Similarity NPC74086
0.5686 Remote Similarity NPC304788
0.5676 Remote Similarity NPC178575
0.5676 Remote Similarity NPC5734
0.5667 Remote Similarity NPC324812
0.5663 Remote Similarity NPC203795
0.5652 Remote Similarity NPC179087
0.5652 Remote Similarity NPC477707
0.5652 Remote Similarity NPC210303
0.5652 Remote Similarity NPC44343
0.5652 Remote Similarity NPC475073
0.5647 Remote Similarity NPC95364
0.5647 Remote Similarity NPC142159
0.5645 Remote Similarity NPC43053
0.5645 Remote Similarity NPC64866
0.5636 Remote Similarity NPC217923
0.5634 Remote Similarity NPC315115
0.5634 Remote Similarity NPC191233

  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 NPC129710 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
0.807 Intermediate Similarity NPD8779 Phase 3
0.7077 Intermediate Similarity NPD6108 Clinical (unspecified phase)
0.6792 Remote Similarity NPD9091 Suspended
0.6792 Remote Similarity NPD9297 Discontinued
0.6575 Remote Similarity NPD4756 Discovery
0.6429 Remote Similarity NPD9090 Phase 3
0.6324 Remote Similarity NPD3704 Approved
0.6234 Remote Similarity NPD5115 Clinical (unspecified phase)
0.6119 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6094 Remote Similarity NPD9287 Clinical (unspecified phase)
0.5938 Remote Similarity NPD9286 Clinical (unspecified phase)
0.5873 Remote Similarity NPD539 Approved
0.5696 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5636 Remote Similarity NPD5783 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