Structure

Physi-Chem Properties

Molecular Weight:  319.21
Volume:  346.889
LogP:  5.282
LogD:  4.064
LogS:  -5.396
# Rotatable Bonds:  8
TPSA:  58.56
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.554
Synthetic Accessibility Score:  3.519
Fsp3:  0.632
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.699
MDCK Permeability:  1.8825929146260023e-05
Pgp-inhibitor:  0.063
Pgp-substrate:  0.194
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.681
Plasma Protein Binding (PPB):  98.18321990966797%
Volume Distribution (VD):  0.693
Pgp-substrate:  1.682035207748413%

ADMET: Metabolism

CYP1A2-inhibitor:  0.765
CYP1A2-substrate:  0.886
CYP2C19-inhibitor:  0.603
CYP2C19-substrate:  0.53
CYP2C9-inhibitor:  0.532
CYP2C9-substrate:  0.693
CYP2D6-inhibitor:  0.67
CYP2D6-substrate:  0.783
CYP3A4-inhibitor:  0.508
CYP3A4-substrate:  0.17

ADMET: Excretion

Clearance (CL):  2.638
Half-life (T1/2):  0.11

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.226
Drug-inuced Liver Injury (DILI):  0.471
AMES Toxicity:  0.7
Rat Oral Acute Toxicity:  0.329
Maximum Recommended Daily Dose:  0.083
Skin Sensitization:  0.613
Carcinogencity:  0.072
Eye Corrosion:  0.003
Eye Irritation:  0.1
Respiratory Toxicity:  0.498

Download Data

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

  Natural Product: NPC116231

Natural Product ID:  NPC116231
Common Name*:   Antidesmone
IUPAC Name:   (5S)-3-methoxy-2-methyl-5-octyl-1,5,6,7-tetrahydroquinoline-4,8-dione
Synonyms:  
Standard InCHIKey:  SJWGGIJOUKBIPF-AWEZNQCLSA-N
Standard InCHI:  InChI=1S/C19H29NO3/c1-4-5-6-7-8-9-10-14-11-12-15(21)17-16(14)18(22)19(23-3)13(2)20-17/h14H,4-12H2,1-3H3,(H,20,22)/t14-/m0/s1
SMILES:  CCCCCCCC[C@H]1CCC(=O)c2c1c(=O)c(c(C)[nH]2)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3342756
PubChem CID:   6426678
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0003671] Aryl alkyl ketones

*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
NPO22669 Waltheria indica Species Malvaceae Eukaryota roots n.a. n.a. PMID[25314007]
NPO22669 Waltheria indica Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[26848627]
NPO40548 Melochia umbellata var. deglabrata Strain Malvaceae Eukaryota n.a. n.a. n.a. PMID[32946697]
NPO22669 Waltheria indica Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[33095014]
NPO22669 Waltheria indica Species Malvaceae 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
NPT839 Cell Line L6 Rattus norvegicus IC50 = 184300.0 nM PMID[568109]
NPT165 Cell Line HeLa Homo sapiens IC50 = 23.4 ug.mL-1 PMID[568110]
NPT81 Cell Line A549 Homo sapiens IC50 = 8400.0 nM PMID[568111]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 6700.0 nM PMID[568111]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 6400.0 nM PMID[568111]
NPT91 Cell Line KB Homo sapiens IC50 = 17700.0 nM PMID[568111]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 > 100000.0 nM PMID[568109]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 14300.0 nM PMID[568109]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 170.0 nM PMID[568109]
NPT2 Others Unspecified Ratio IC50 = 1084.3 n.a. PMID[568109]
NPT20 Organism Candida albicans Candida albicans MIC = 16.0 ug.mL-1 PMID[568110]
NPT19 Organism Escherichia coli Escherichia coli MIC > 32.0 ug.mL-1 PMID[568110]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 32.0 ug.mL-1 PMID[568110]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC > 32.0 ug.mL-1 PMID[568110]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC = 4.0 ug.mL-1 PMID[568110]
NPT186 Organism Candida tropicalis Candida tropicalis MIC > 32.0 ug.mL-1 PMID[568110]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MIC = 16.0 ug.mL-1 PMID[568110]
NPT554 Organism Candida glabrata Candida glabrata MIC > 32.0 ug.mL-1 PMID[568110]
NPT20 Organism Candida albicans Candida albicans MIC = 32.0 ug.mL-1 PMID[568110]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 32.0 ug.mL-1 PMID[568110]
NPT2 Others Unspecified Selectivity Index = 0.7 n.a. PMID[568110]
NPT2 Others Unspecified IC50 = 8600.0 nM PMID[568111]
NPT2 Others Unspecified Ratio IC50 = 2.0 n.a. PMID[568111]

☑ 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 NPC116231 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
0.9756 High Similarity NPC472161
0.8837 High Similarity NPC472136
0.8696 High Similarity NPC472162
0.7917 Intermediate Similarity NPC472167
0.7917 Intermediate Similarity NPC472166
0.699 Remote Similarity NPC34193
0.6786 Remote Similarity NPC472164
0.6739 Remote Similarity NPC23778
0.6636 Remote Similarity NPC87919
0.663 Remote Similarity NPC283087
0.6606 Remote Similarity NPC24596
0.66 Remote Similarity NPC236322
0.6574 Remote Similarity NPC185929
0.6526 Remote Similarity NPC474085
0.6486 Remote Similarity NPC72688
0.646 Remote Similarity NPC5485
0.6429 Remote Similarity NPC475614
0.6395 Remote Similarity NPC34622
0.6395 Remote Similarity NPC474400
0.6392 Remote Similarity NPC8091
0.6348 Remote Similarity NPC7905
0.6348 Remote Similarity NPC315652
0.6322 Remote Similarity NPC98897
0.6316 Remote Similarity NPC475681
0.6293 Remote Similarity NPC27413
0.6293 Remote Similarity NPC59751
0.6293 Remote Similarity NPC271621
0.6279 Remote Similarity NPC57463
0.6279 Remote Similarity NPC151728
0.6263 Remote Similarity NPC133652
0.6263 Remote Similarity NPC6185
0.6263 Remote Similarity NPC241512
0.6263 Remote Similarity NPC8518
0.6263 Remote Similarity NPC132228
0.6263 Remote Similarity NPC263997
0.6261 Remote Similarity NPC176336
0.625 Remote Similarity NPC16119
0.6239 Remote Similarity NPC296361
0.6238 Remote Similarity NPC318578
0.6216 Remote Similarity NPC176773
0.618 Remote Similarity NPC243272
0.618 Remote Similarity NPC474619
0.6179 Remote Similarity NPC472165
0.617 Remote Similarity NPC92080
0.616 Remote Similarity NPC315011
0.6147 Remote Similarity NPC251884
0.6134 Remote Similarity NPC473808
0.6134 Remote Similarity NPC315110
0.6117 Remote Similarity NPC223093
0.6111 Remote Similarity NPC263382
0.6111 Remote Similarity NPC134385
0.6111 Remote Similarity NPC125578
0.6111 Remote Similarity NPC146376
0.61 Remote Similarity NPC90287
0.6087 Remote Similarity NPC474539
0.6083 Remote Similarity NPC315915
0.6064 Remote Similarity NPC175079
0.6061 Remote Similarity NPC471595
0.6044 Remote Similarity NPC94488
0.6044 Remote Similarity NPC262673
0.6042 Remote Similarity NPC30321
0.604 Remote Similarity NPC203795
0.6036 Remote Similarity NPC9436
0.602 Remote Similarity NPC312419
0.602 Remote Similarity NPC478262
0.6 Remote Similarity NPC26504
0.5978 Remote Similarity NPC94743
0.5978 Remote Similarity NPC291062
0.5978 Remote Similarity NPC173321
0.5962 Remote Similarity NPC475823
0.5962 Remote Similarity NPC474209
0.5957 Remote Similarity NPC264178
0.5957 Remote Similarity NPC147438
0.5941 Remote Similarity NPC474680
0.5941 Remote Similarity NPC76283
0.5941 Remote Similarity NPC478245
0.5941 Remote Similarity NPC2640
0.593 Remote Similarity NPC473494
0.5922 Remote Similarity NPC53454
0.5918 Remote Similarity NPC108955
0.5905 Remote Similarity NPC166110
0.5893 Remote Similarity NPC133420
0.5882 Remote Similarity NPC322672
0.5876 Remote Similarity NPC469996
0.5876 Remote Similarity NPC478247
0.5876 Remote Similarity NPC478246
0.5876 Remote Similarity NPC476808
0.5865 Remote Similarity NPC280833
0.5859 Remote Similarity NPC474353
0.5859 Remote Similarity NPC225515
0.5859 Remote Similarity NPC99308
0.5859 Remote Similarity NPC55869
0.5849 Remote Similarity NPC248193
0.584 Remote Similarity NPC473249
0.5825 Remote Similarity NPC473525
0.5816 Remote Similarity NPC192329
0.5816 Remote Similarity NPC476177
0.58 Remote Similarity NPC103486
0.5784 Remote Similarity NPC319913
0.5778 Remote Similarity NPC61473
0.5773 Remote Similarity NPC472300
0.5769 Remote Similarity NPC478261
0.5769 Remote Similarity NPC475001
0.5769 Remote Similarity NPC478260
0.5769 Remote Similarity NPC478259
0.5769 Remote Similarity NPC307298
0.5769 Remote Similarity NPC185059
0.5758 Remote Similarity NPC18955
0.5755 Remote Similarity NPC248913
0.5743 Remote Similarity NPC288281
0.5743 Remote Similarity NPC105803
0.5741 Remote Similarity NPC31021
0.5739 Remote Similarity NPC220730
0.5738 Remote Similarity NPC13351
0.5738 Remote Similarity NPC139867
0.573 Remote Similarity NPC477830
0.573 Remote Similarity NPC143168
0.573 Remote Similarity NPC53109
0.5714 Remote Similarity NPC58200
0.5714 Remote Similarity NPC473955
0.5714 Remote Similarity NPC142159
0.5714 Remote Similarity NPC95364
0.5702 Remote Similarity NPC233256
0.5702 Remote Similarity NPC195841
0.57 Remote Similarity NPC149237
0.57 Remote Similarity NPC475833
0.5686 Remote Similarity NPC60951
0.5686 Remote Similarity NPC474359
0.5673 Remote Similarity NPC220930
0.5673 Remote Similarity NPC272039
0.567 Remote Similarity NPC40353
0.567 Remote Similarity NPC110725
0.567 Remote Similarity NPC470525
0.5667 Remote Similarity NPC7029
0.566 Remote Similarity NPC478258
0.566 Remote Similarity NPC113393
0.566 Remote Similarity NPC478257
0.5657 Remote Similarity NPC276647
0.5657 Remote Similarity NPC27817
0.5657 Remote Similarity NPC268502
0.5657 Remote Similarity NPC622
0.5657 Remote Similarity NPC254996
0.5648 Remote Similarity NPC212812
0.5644 Remote Similarity NPC321289
0.5644 Remote Similarity NPC327969
0.5644 Remote Similarity NPC473810
0.5631 Remote Similarity NPC32037
0.5631 Remote Similarity NPC470177
0.5625 Remote Similarity NPC470299
0.5625 Remote Similarity NPC77703
0.5625 Remote Similarity NPC119326
0.562 Remote Similarity NPC316325
0.5614 Remote Similarity NPC472616
0.5607 Remote Similarity NPC193396
0.5607 Remote Similarity NPC470036
0.5607 Remote Similarity NPC26865
0.5607 Remote Similarity NPC174167
0.5607 Remote Similarity NPC32944
0.5603 Remote Similarity NPC470535
0.56 Remote Similarity NPC474956
0.56 Remote Similarity NPC2482
0.56 Remote Similarity NPC250632
0.56 Remote Similarity NPC304795

  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 NPC116231 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
0.6696 Remote Similarity NPD7299 Clinical (unspecified phase)
0.625 Remote Similarity NPD6108 Clinical (unspecified phase)
0.625 Remote Similarity NPD3704 Approved
0.616 Remote Similarity NPD2101 Approved
0.6134 Remote Similarity NPD7196 Clinical (unspecified phase)
0.6083 Remote Similarity NPD7739 Clinical (unspecified phase)
0.6033 Remote Similarity NPD7623 Phase 3
0.6033 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5918 Remote Similarity NPD4695 Discontinued
0.59 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5876 Remote Similarity NPD3617 Approved
0.5862 Remote Similarity NPD7116 Clinical (unspecified phase)
0.584 Remote Similarity NPD7746 Phase 1
0.584 Remote Similarity NPD7747 Phase 1
0.5778 Remote Similarity NPD7341 Phase 2
0.5738 Remote Similarity NPD1689 Approved
0.573 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5656 Remote Similarity NPD2132 Phase 3
0.562 Remote Similarity NPD7500 Approved
0.5619 Remote Similarity NPD5737 Approved
0.5619 Remote Similarity NPD6672 Approved
0.5612 Remote Similarity NPD4756 Discovery

  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