Structure

Physi-Chem Properties

Molecular Weight:  139.11
Volume:  148.789
LogP:  0.14
LogD:  -0.391
LogS:  0.924
# Rotatable Bonds:  3
TPSA:  31.92
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.661
Synthetic Accessibility Score:  2.816
Fsp3:  0.571
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.691
MDCK Permeability:  4.033131062897155e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.619
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.959
Plasma Protein Binding (PPB):  17.16550064086914%
Volume Distribution (VD):  1.531
Pgp-substrate:  90.04890441894531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.58
CYP2C19-inhibitor:  0.041
CYP2C19-substrate:  0.5
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.367
CYP2D6-inhibitor:  0.565
CYP2D6-substrate:  0.265
CYP3A4-inhibitor:  0.21
CYP3A4-substrate:  0.153

ADMET: Excretion

Clearance (CL):  8.402
Half-life (T1/2):  0.854

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.248
Drug-inuced Liver Injury (DILI):  0.052
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.425
Maximum Recommended Daily Dose:  0.716
Skin Sensitization:  0.94
Carcinogencity:  0.014
Eye Corrosion:  0.512
Eye Irritation:  0.506
Respiratory Toxicity:  0.89

Download Data

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

  Natural Product: NPC155498

Natural Product ID:  NPC155498
Common Name*:   2-(1H-Imidazol-5-Yl)-N,N-Dimethylethanamine
IUPAC Name:   2-(1H-imidazol-5-yl)-N,N-dimethylethanamine
Synonyms:  
Standard InCHIKey:  ZJDIMSMQXMWMCF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H13N3/c1-10(2)4-3-7-5-8-6-9-7/h5-6H,3-4H2,1-2H3,(H,8,9)
SMILES:  CN(C)CCc1cnc[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL12704
PubChem CID:   12656
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0003899] Aralkylamines

*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
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. seed n.a. PMID[10075120]
NPO7344 Spiraea prunifolia Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[11473429]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[16499335]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[17228877]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[18484537]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[19615910]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[29323912]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. root n.a. PMID[731398]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[731398]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. rhizome n.a. PMID[7714541]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[7760071]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. rhizome n.a. PMID[7798964]
NPO19895 Plectranthus hereroensis Species Lamiaceae Eukaryota Roots n.a. n.a. PMID[7931371]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. PMID[7964801]
NPO23356 Ascodesmis sphaerospora Species Ascodesmidaceae Eukaryota n.a. n.a. n.a. PMID[9868168]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23588 Ursinia anthemoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7344 Spiraea prunifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23588 Ursinia anthemoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17492 Amomum reticulatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23356 Ascodesmis sphaerospora Species Ascodesmidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19895 Plectranthus hereroensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24396 Grosvenoria rimbachii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15572 Espeletiopsis purpurascens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23398 Caralluma russeliana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23911 Alpinia officinarum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24280 Helianthus californicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24038 Casimiroa edulis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23822 Polypodium aureum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23628 Imperata cylindrica Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23490 Dalbergia monetaria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9814 Lactarius fuliginosus Species Russulaceae 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
NPT4288 Individual Protein Histamine H1 receptor Cavia porcellus Activity = 44.0 n.a. PMID[511276]
NPT4289 Individual Protein Histamine H2 receptor Cavia porcellus Activity = 51.0 n.a. PMID[511276]
NPT29 Organism Rattus norvegicus Rattus norvegicus Ratio_EC50 = 170.0 n.a. PMID[511276]
NPT29 Organism Rattus norvegicus Rattus norvegicus pD2 = 7.3 n.a. PMID[511276]

☑ 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 NPC155498 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
0.9794 High Similarity NPC111132
0.9388 High Similarity NPC187191
0.9388 High Similarity NPC326248
0.9072 High Similarity NPC9639
0.8962 High Similarity NPC327613
0.819 Intermediate Similarity NPC273327
0.8051 Intermediate Similarity NPC180462
0.7731 Intermediate Similarity NPC15566
0.7642 Intermediate Similarity NPC25465
0.75 Intermediate Similarity NPC235501
0.748 Intermediate Similarity NPC18223
0.748 Intermediate Similarity NPC237812
0.7347 Intermediate Similarity NPC237936
0.7308 Intermediate Similarity NPC286696
0.7308 Intermediate Similarity NPC185903
0.7288 Intermediate Similarity NPC68938
0.7188 Intermediate Similarity NPC126634
0.7164 Intermediate Similarity NPC197068
0.7037 Intermediate Similarity NPC327477
0.7008 Intermediate Similarity NPC243319
0.697 Remote Similarity NPC210947
0.693 Remote Similarity NPC476099
0.6881 Remote Similarity NPC51000
0.6838 Remote Similarity NPC174020
0.6761 Remote Similarity NPC60537
0.6738 Remote Similarity NPC282531
0.6698 Remote Similarity NPC190949
0.6617 Remote Similarity NPC470140
0.6579 Remote Similarity NPC293163
0.6565 Remote Similarity NPC470138
0.6496 Remote Similarity NPC18335
0.6475 Remote Similarity NPC313547
0.6471 Remote Similarity NPC470139
0.641 Remote Similarity NPC59314
0.629 Remote Similarity NPC148385
0.626 Remote Similarity NPC41958
0.622 Remote Similarity NPC252603
0.6218 Remote Similarity NPC476562
0.6214 Remote Similarity NPC8590
0.619 Remote Similarity NPC278549
0.6182 Remote Similarity NPC277608
0.6176 Remote Similarity NPC204104
0.6148 Remote Similarity NPC57279
0.6147 Remote Similarity NPC76536
0.6139 Remote Similarity NPC477119
0.6117 Remote Similarity NPC270637
0.6102 Remote Similarity NPC87981
0.6102 Remote Similarity NPC174114
0.6098 Remote Similarity NPC4837
0.6098 Remote Similarity NPC312187
0.605 Remote Similarity NPC476561
0.6036 Remote Similarity NPC262236
0.6032 Remote Similarity NPC63433
0.6019 Remote Similarity NPC100312
0.5987 Remote Similarity NPC300238
0.5982 Remote Similarity NPC326364
0.5957 Remote Similarity NPC216159
0.5938 Remote Similarity NPC189314
0.5915 Remote Similarity NPC477118
0.5882 Remote Similarity NPC246193
0.5879 Remote Similarity NPC477120
0.5862 Remote Similarity NPC196580
0.5814 Remote Similarity NPC240084
0.5764 Remote Similarity NPC315642
0.5764 Remote Similarity NPC74306
0.5763 Remote Similarity NPC476128
0.5714 Remote Similarity NPC42483
0.5703 Remote Similarity NPC199790
0.5652 Remote Similarity NPC104011
0.5649 Remote Similarity NPC158847
0.5645 Remote Similarity NPC119133
0.5634 Remote Similarity NPC470141
0.5614 Remote Similarity NPC201900
0.5614 Remote Similarity NPC313504
0.5606 Remote Similarity NPC327579

  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 NPC155498 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
0.9794 High Similarity NPD8859 Approved
0.9794 High Similarity NPD8861 Approved
0.9794 High Similarity NPD8862 Approved
0.8796 High Similarity NPD9132 Discontinued
0.8051 Intermediate Similarity NPD300 Approved
0.8034 Intermediate Similarity NPD1390 Phase 1
0.8034 Intermediate Similarity NPD1388 Phase 1
0.8034 Intermediate Similarity NPD1389 Clinical (unspecified phase)
0.7769 Intermediate Similarity NPD1807 Clinical (unspecified phase)
0.748 Intermediate Similarity NPD9133 Approved
0.748 Intermediate Similarity NPD9628 Approved
0.7347 Intermediate Similarity NPD8185 Discontinued
0.7347 Intermediate Similarity NPD8186 Phase 1
0.7297 Intermediate Similarity NPD340 Approved
0.7297 Intermediate Similarity NPD341 Approved
0.7273 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.7197 Intermediate Similarity NPD9183 Clinical (unspecified phase)
0.7197 Intermediate Similarity NPD1451 Approved
0.7103 Intermediate Similarity NPD9210 Phase 2
0.709 Intermediate Similarity NPD9627 Approved
0.7015 Intermediate Similarity NPD3706 Clinical (unspecified phase)
0.7008 Intermediate Similarity NPD9081 Clinical (unspecified phase)
0.6881 Remote Similarity NPD8838 Approved
0.6809 Remote Similarity NPD1731 Clinical (unspecified phase)
0.6783 Remote Similarity NPD2604 Approved
0.6761 Remote Similarity NPD2180 Approved
0.669 Remote Similarity NPD1030 Approved
0.669 Remote Similarity NPD1029 Clinical (unspecified phase)
0.669 Remote Similarity NPD1027 Approved
0.6667 Remote Similarity NPD3697 Discontinued
0.6667 Remote Similarity NPD875 Clinical (unspecified phase)
0.6637 Remote Similarity NPD9193 Approved
0.6637 Remote Similarity NPD9194 Approved
0.6599 Remote Similarity NPD5768 Phase 2
0.6599 Remote Similarity NPD3130 Discontinued
0.6557 Remote Similarity NPD757 Phase 3
0.65 Remote Similarity NPD8954 Approved
0.65 Remote Similarity NPD8955 Approved
0.6496 Remote Similarity NPD8836 Approved
0.6483 Remote Similarity NPD1303 Phase 1
0.6439 Remote Similarity NPD9650 Phase 3
0.641 Remote Similarity NPD8837 Clinical (unspecified phase)
0.64 Remote Similarity NPD9360 Approved
0.6395 Remote Similarity NPD1290 Phase 2
0.637 Remote Similarity NPD695 Discontinued
0.637 Remote Similarity NPD576 Discontinued
0.6333 Remote Similarity NPD1122 Clinical (unspecified phase)
0.6309 Remote Similarity NPD1042 Clinical (unspecified phase)
0.6299 Remote Similarity NPD3105 Discontinued
0.6286 Remote Similarity NPD8584 Approved
0.624 Remote Similarity NPD163 Approved
0.6231 Remote Similarity NPD579 Clinical (unspecified phase)
0.622 Remote Similarity NPD9288 Approved
0.622 Remote Similarity NPD76 Approved
0.622 Remote Similarity NPD9289 Approved
0.622 Remote Similarity NPD9292 Approved
0.6218 Remote Similarity NPD3108 Clinical (unspecified phase)
0.6194 Remote Similarity NPD3347 Clinical (unspecified phase)
0.617 Remote Similarity NPD174 Discontinued
0.6118 Remote Similarity NPD1016 Phase 2
0.6118 Remote Similarity NPD1015 Phase 2
0.6104 Remote Similarity NPD2478 Clinical (unspecified phase)
0.6077 Remote Similarity NPD306 Approved
0.6056 Remote Similarity NPD566 Approved
0.6056 Remote Similarity NPD567 Approved
0.6056 Remote Similarity NPD568 Approved
0.6039 Remote Similarity NPD1333 Phase 3
0.6015 Remote Similarity NPD515 Phase 1
0.5987 Remote Similarity NPD1567 Clinical (unspecified phase)
0.5984 Remote Similarity NPD1816 Clinical (unspecified phase)
0.5951 Remote Similarity NPD2457 Phase 2
0.5951 Remote Similarity NPD2456 Phase 2
0.595 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5938 Remote Similarity NPD8831 Approved
0.5938 Remote Similarity NPD8833 Approved
0.5929 Remote Similarity NPD799 Phase 1
0.592 Remote Similarity NPD9412 Discontinued
0.5901 Remote Similarity NPD1327 Discontinued
0.5901 Remote Similarity NPD2930 Clinical (unspecified phase)
0.5891 Remote Similarity NPD237 Clinical (unspecified phase)
0.5873 Remote Similarity NPD9373 Approved
0.5846 Remote Similarity NPD307 Approved
0.5828 Remote Similarity NPD4649 Clinical (unspecified phase)
0.5814 Remote Similarity NPD1368 Approved
0.5794 Remote Similarity NPD9375 Discontinued
0.5789 Remote Similarity NPD3405 Phase 3
0.5781 Remote Similarity NPD9374 Approved
0.5764 Remote Similarity NPD582 Approved
0.5755 Remote Similarity NPD209 Clinical (unspecified phase)
0.5742 Remote Similarity NPD1288 Clinical (unspecified phase)
0.5735 Remote Similarity NPD870 Clinical (unspecified phase)
0.5732 Remote Similarity NPD2135 Approved
0.5732 Remote Similarity NPD1895 Discontinued
0.5732 Remote Similarity NPD2134 Approved
0.5732 Remote Similarity NPD2136 Approved
0.5714 Remote Similarity NPD9724 Phase 1
0.569 Remote Similarity NPD8786 Approved
0.5689 Remote Similarity NPD2793 Discontinued
0.5682 Remote Similarity NPD9409 Discontinued
0.5678 Remote Similarity NPD9189 Discontinued
0.5658 Remote Similarity NPD1257 Approved
0.5655 Remote Similarity NPD1117 Clinical (unspecified phase)
0.5649 Remote Similarity NPD9606 Approved
0.5647 Remote Similarity NPD3419 Clinical (unspecified phase)
0.5645 Remote Similarity NPD9291 Approved
0.5643 Remote Similarity NPD9083 Clinical (unspecified phase)
0.5643 Remote Similarity NPD1058 Discontinued
0.5633 Remote Similarity NPD1313 Approved
0.5625 Remote Similarity NPD2875 Clinical (unspecified phase)
0.561 Remote Similarity NPD3341 Clinical (unspecified phase)
0.5606 Remote Similarity NPD9607 Approved
0.5603 Remote Similarity NPD8787 Clinical (unspecified phase)
0.5603 Remote Similarity NPD9484 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