Structure

Physi-Chem Properties

Molecular Weight:  335.25
Volume:  366.821
LogP:  4.829
LogD:  3.594
LogS:  -4.281
# Rotatable Bonds:  9
TPSA:  51.32
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.646
Synthetic Accessibility Score:  3.666
Fsp3:  0.75
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:  -4.808
MDCK Permeability:  1.6250436601694673e-05
Pgp-inhibitor:  0.278
Pgp-substrate:  0.338
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.53
Plasma Protein Binding (PPB):  96.7077865600586%
Volume Distribution (VD):  0.77
Pgp-substrate:  2.107818603515625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.331
CYP1A2-substrate:  0.975
CYP2C19-inhibitor:  0.512
CYP2C19-substrate:  0.929
CYP2C9-inhibitor:  0.516
CYP2C9-substrate:  0.83
CYP2D6-inhibitor:  0.204
CYP2D6-substrate:  0.59
CYP3A4-inhibitor:  0.702
CYP3A4-substrate:  0.729

ADMET: Excretion

Clearance (CL):  3.098
Half-life (T1/2):  0.169

ADMET: Toxicity

hERG Blockers:  0.255
Human Hepatotoxicity (H-HT):  0.221
Drug-inuced Liver Injury (DILI):  0.251
AMES Toxicity:  0.15
Rat Oral Acute Toxicity:  0.851
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.916
Carcinogencity:  0.273
Eye Corrosion:  0.019
Eye Irritation:  0.09
Respiratory Toxicity:  0.97

Download Data

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

  Natural Product: NPC472162

Natural Product ID:  NPC472162
Common Name*:   HFYVJDDISIDMQP-JKSUJKDBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HFYVJDDISIDMQP-JKSUJKDBSA-N
Standard InCHI:  InChI=1S/C20H33NO3/c1-5-6-7-8-9-10-11-15-12-13-16(23-3)18-17(15)19(22)20(24-4)14(2)21-18/h15-16H,5-13H2,1-4H3,(H,21,22)/t15-,16+/m0/s1
SMILES:  CCCCCCCC[C@H]1CC[C@H](c2c1c(=O)c(c([nH]2)C)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3342749
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0000128] Alkyl aryl ethers

*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]
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 = 910.0 nM PMID[521218]
NPT165 Cell Line HeLa Homo sapiens IC50 = 20.0 ug.mL-1 PMID[521219]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 38500.0 nM PMID[521218]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 = 80300.0 nM PMID[521218]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 230.0 nM PMID[521218]
NPT2 Others Unspecified Ratio IC50 = 4.0 n.a. PMID[521218]
NPT20 Organism Candida albicans Candida albicans MIC = 8.0 ug.mL-1 PMID[521219]
NPT19 Organism Escherichia coli Escherichia coli MIC > 32.0 ug.mL-1 PMID[521219]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC > 32.0 ug.mL-1 PMID[521219]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC > 32.0 ug.mL-1 PMID[521219]
NPT186 Organism Candida tropicalis Candida tropicalis MIC > 32.0 ug.mL-1 PMID[521219]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MIC > 32.0 ug.mL-1 PMID[521219]
NPT554 Organism Candida glabrata Candida glabrata MIC > 32.0 ug.mL-1 PMID[521219]
NPT20 Organism Candida albicans Candida albicans MIC = 4.0 ug.mL-1 PMID[521219]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 32.0 ug.mL-1 PMID[521219]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 32.0 ug.mL-1 PMID[521219]
NPT2 Others Unspecified Selectivity Index = 5.0 n.a. PMID[521219]

☑ 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 NPC472162 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
0.9149 High Similarity NPC472167
0.8889 High Similarity NPC472161
0.8696 High Similarity NPC116231
0.8367 Intermediate Similarity NPC472166
0.828 Intermediate Similarity NPC472136
0.7107 Intermediate Similarity NPC472165
0.687 Remote Similarity NPC5485
0.6752 Remote Similarity NPC315652
0.6752 Remote Similarity NPC7905
0.6695 Remote Similarity NPC27413
0.6695 Remote Similarity NPC59751
0.6695 Remote Similarity NPC271621
0.6639 Remote Similarity NPC296361
0.6529 Remote Similarity NPC473808
0.6475 Remote Similarity NPC315915
0.646 Remote Similarity NPC87919
0.6349 Remote Similarity NPC317654
0.6349 Remote Similarity NPC96010
0.6339 Remote Similarity NPC314792
0.6339 Remote Similarity NPC34193
0.6333 Remote Similarity NPC472164
0.6321 Remote Similarity NPC280833
0.6316 Remote Similarity NPC133420
0.6299 Remote Similarity NPC478136
0.6296 Remote Similarity NPC248193
0.6262 Remote Similarity NPC113393
0.6226 Remote Similarity NPC307298
0.6204 Remote Similarity NPC166110
0.62 Remote Similarity NPC23778
0.6174 Remote Similarity NPC477000
0.6174 Remote Similarity NPC477001
0.6154 Remote Similarity NPC474359
0.6154 Remote Similarity NPC220730
0.6154 Remote Similarity NPC60951
0.614 Remote Similarity NPC251884
0.6121 Remote Similarity NPC185929
0.61 Remote Similarity NPC283087
0.6094 Remote Similarity NPC473249
0.6077 Remote Similarity NPC478139
0.6075 Remote Similarity NPC143025
0.6075 Remote Similarity NPC478261
0.6075 Remote Similarity NPC478260
0.6075 Remote Similarity NPC478259
0.6075 Remote Similarity NPC53454
0.6068 Remote Similarity NPC176773
0.6058 Remote Similarity NPC8091
0.6038 Remote Similarity NPC220478
0.6031 Remote Similarity NPC315011
0.6019 Remote Similarity NPC95364
0.6019 Remote Similarity NPC142159
0.6019 Remote Similarity NPC474085
0.6019 Remote Similarity NPC312419
0.6017 Remote Similarity NPC24596
0.6016 Remote Similarity NPC316325
0.6 Remote Similarity NPC271652
0.6 Remote Similarity NPC476597
0.6 Remote Similarity NPC476598
0.598 Remote Similarity NPC475681
0.5963 Remote Similarity NPC236322
0.5957 Remote Similarity NPC98897
0.5946 Remote Similarity NPC476596
0.5943 Remote Similarity NPC133652
0.5943 Remote Similarity NPC475614
0.5941 Remote Similarity NPC41780
0.5941 Remote Similarity NPC471225
0.5941 Remote Similarity NPC187568
0.5917 Remote Similarity NPC72688
0.5913 Remote Similarity NPC77703
0.5909 Remote Similarity NPC32944
0.5909 Remote Similarity NPC190442
0.5909 Remote Similarity NPC193396
0.5905 Remote Similarity NPC193198
0.5905 Remote Similarity NPC222358
0.5905 Remote Similarity NPC288281
0.5895 Remote Similarity NPC16119
0.5882 Remote Similarity NPC471220
0.5868 Remote Similarity NPC44733
0.5856 Remote Similarity NPC229976
0.5851 Remote Similarity NPC474400
0.5851 Remote Similarity NPC34622
0.5847 Remote Similarity NPC271269
0.5847 Remote Similarity NPC154601
0.5839 Remote Similarity NPC473955
0.5833 Remote Similarity NPC272039
0.5833 Remote Similarity NPC220930
0.5833 Remote Similarity NPC474619
0.5833 Remote Similarity NPC307165
0.5825 Remote Similarity NPC471299
0.5818 Remote Similarity NPC471818
0.5816 Remote Similarity NPC173321
0.581 Remote Similarity NPC10080
0.581 Remote Similarity NPC123908
0.5798 Remote Similarity NPC251330
0.5798 Remote Similarity NPC467022
0.5794 Remote Similarity NPC8518
0.5794 Remote Similarity NPC6185
0.5794 Remote Similarity NPC132228
0.5794 Remote Similarity NPC263997
0.5794 Remote Similarity NPC96621
0.5794 Remote Similarity NPC90287
0.5794 Remote Similarity NPC241512
0.5794 Remote Similarity NPC476678
0.5789 Remote Similarity NPC241426
0.578 Remote Similarity NPC475001
0.578 Remote Similarity NPC185059
0.578 Remote Similarity NPC318578
0.5776 Remote Similarity NPC471699
0.5776 Remote Similarity NPC469851
0.5773 Remote Similarity NPC146376
0.5773 Remote Similarity NPC263382
0.5773 Remote Similarity NPC125578
0.5766 Remote Similarity NPC248913
0.5763 Remote Similarity NPC472616
0.5758 Remote Similarity NPC198644
0.5758 Remote Similarity NPC311244
0.5758 Remote Similarity NPC324722
0.5758 Remote Similarity NPC97861
0.5758 Remote Similarity NPC474539
0.5755 Remote Similarity NPC470047
0.5755 Remote Similarity NPC474703
0.5755 Remote Similarity NPC470046
0.5752 Remote Similarity NPC91408
0.5752 Remote Similarity NPC470974
0.5752 Remote Similarity NPC470978
0.5752 Remote Similarity NPC295347
0.5748 Remote Similarity NPC477143
0.5748 Remote Similarity NPC477140
0.5748 Remote Similarity NPC13351
0.5745 Remote Similarity NPC57463
0.5745 Remote Similarity NPC151728
0.5741 Remote Similarity NPC203795
0.5739 Remote Similarity NPC166770
0.5728 Remote Similarity NPC231739
0.5728 Remote Similarity NPC315765
0.5728 Remote Similarity NPC475994
0.5727 Remote Similarity NPC210216
0.5727 Remote Similarity NPC284561
0.5726 Remote Similarity NPC469423
0.5726 Remote Similarity NPC176336
0.5726 Remote Similarity NPC469598
0.5726 Remote Similarity NPC80781
0.5714 Remote Similarity NPC471325
0.5714 Remote Similarity NPC282293
0.5714 Remote Similarity NPC233256
0.5714 Remote Similarity NPC478262
0.5714 Remote Similarity NPC195841
0.5714 Remote Similarity NPC94488
0.5714 Remote Similarity NPC215507
0.5714 Remote Similarity NPC472615
0.5702 Remote Similarity NPC218602
0.5701 Remote Similarity NPC30486
0.569 Remote Similarity NPC215253
0.569 Remote Similarity NPC185253
0.5688 Remote Similarity NPC103743
0.5688 Remote Similarity NPC113370
0.5688 Remote Similarity NPC476079
0.5686 Remote Similarity NPC92080
0.5686 Remote Similarity NPC271070
0.5686 Remote Similarity NPC473223
0.5686 Remote Similarity NPC40353
0.5686 Remote Similarity NPC27205
0.5678 Remote Similarity NPC473144
0.5678 Remote Similarity NPC25666
0.5678 Remote Similarity NPC297281
0.5678 Remote Similarity NPC320154
0.5678 Remote Similarity NPC271059
0.5676 Remote Similarity NPC212679
0.5676 Remote Similarity NPC474209
0.5676 Remote Similarity NPC213636
0.5676 Remote Similarity NPC475823
0.5676 Remote Similarity NPC223093
0.5676 Remote Similarity NPC220454
0.5676 Remote Similarity NPC469595
0.5676 Remote Similarity NPC471399
0.5676 Remote Similarity NPC253177
0.5676 Remote Similarity NPC280592
0.5673 Remote Similarity NPC254996
0.5673 Remote Similarity NPC268502
0.5673 Remote Similarity NPC622
0.5673 Remote Similarity NPC281138
0.5673 Remote Similarity NPC476177
0.5673 Remote Similarity NPC276647
0.567 Remote Similarity NPC243272
0.5664 Remote Similarity NPC474882
0.5664 Remote Similarity NPC212812
0.5664 Remote Similarity NPC471674
0.5664 Remote Similarity NPC148463
0.5664 Remote Similarity NPC201899
0.5662 Remote Similarity NPC239252
0.5662 Remote Similarity NPC473703
0.5657 Remote Similarity NPC291062
0.5657 Remote Similarity NPC94743
0.5652 Remote Similarity NPC208094
0.5652 Remote Similarity NPC134083
0.5648 Remote Similarity NPC2640
0.5648 Remote Similarity NPC471060
0.5648 Remote Similarity NPC189311
0.5648 Remote Similarity NPC478245
0.5648 Remote Similarity NPC470048
0.5644 Remote Similarity NPC264178

  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 NPC472162 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
0.6949 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6341 Remote Similarity NPD7739 Clinical (unspecified phase)
0.629 Remote Similarity NPD7624 Clinical (unspecified phase)
0.629 Remote Similarity NPD7623 Phase 3
0.6271 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6094 Remote Similarity NPD7747 Phase 1
0.6094 Remote Similarity NPD7746 Phase 1
0.6031 Remote Similarity NPD2101 Approved
0.6016 Remote Similarity NPD7500 Approved
0.5895 Remote Similarity NPD3704 Approved
0.5895 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5769 Remote Similarity NPD6637 Approved
0.5645 Remote Similarity NPD1376 Discontinued
0.563 Remote Similarity NPD6845 Suspended
0.5625 Remote Similarity NPD1689 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