Structure

Physi-Chem Properties

Molecular Weight:  154.07
Volume:  152.736
LogP:  -0.004
LogD:  0.157
LogS:  0.366
# Rotatable Bonds:  4
TPSA:  54.98
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.645
Synthetic Accessibility Score:  2.635
Fsp3:  0.429
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:  -4.416
MDCK Permeability:  9.230114301317371e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.924
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.495

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.673
Plasma Protein Binding (PPB):  16.335227966308594%
Volume Distribution (VD):  0.97
Pgp-substrate:  83.06356811523438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.33
CYP1A2-substrate:  0.171
CYP2C19-inhibitor:  0.32
CYP2C19-substrate:  0.226
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.255
CYP2D6-inhibitor:  0.307
CYP2D6-substrate:  0.02
CYP3A4-inhibitor:  0.48
CYP3A4-substrate:  0.211

ADMET: Excretion

Clearance (CL):  9.685
Half-life (T1/2):  0.936

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.607
Drug-inuced Liver Injury (DILI):  0.593
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.04
Maximum Recommended Daily Dose:  0.452
Skin Sensitization:  0.919
Carcinogencity:  0.017
Eye Corrosion:  0.029
Eye Irritation:  0.83
Respiratory Toxicity:  0.051

Download Data

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

  Natural Product: NPC25465

Natural Product ID:  NPC25465
Common Name*:   Methyl 3-(1H-Imidazol-5-Yl)Propanoate
IUPAC Name:   methyl 3-(1H-imidazol-5-yl)propanoate
Synonyms:  
Standard InCHIKey:  YFEPBWKUBQUBKL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10N2O2/c1-11-7(10)3-2-6-4-8-5-9-6/h4-5H,2-3H2,1H3,(H,8,9)
SMILES:  COC(=O)CCc1cnc[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1780252
PubChem CID:   565491
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0001227] Imidazolyl carboxylic acids and derivatives

*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
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. PMID[20488699]
NPO9032 Geotrichum candidum Species Dipodascaceae 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
NPT2 Others Unspecified IC50 = 5200.0 nM PMID[461174]

☑ 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 NPC25465 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
0.9512 High Similarity NPC235501
0.9141 High Similarity NPC18223
0.9141 High Similarity NPC237812
0.8931 High Similarity NPC185903
0.8931 High Similarity NPC286696
0.8806 High Similarity NPC174020
0.8692 High Similarity NPC126634
0.8603 High Similarity NPC327477
0.8433 Intermediate Similarity NPC210947
0.8346 Intermediate Similarity NPC470140
0.8295 Intermediate Similarity NPC180462
0.8281 Intermediate Similarity NPC15566
0.8162 Intermediate Similarity NPC470139
0.8045 Intermediate Similarity NPC470138
0.7755 Intermediate Similarity NPC60537
0.7642 Intermediate Similarity NPC155498
0.7623 Intermediate Similarity NPC111132
0.75 Intermediate Similarity NPC327613
0.7333 Intermediate Similarity NPC9639
0.7254 Intermediate Similarity NPC470141
0.7177 Intermediate Similarity NPC187191
0.7177 Intermediate Similarity NPC326248
0.695 Remote Similarity NPC243319
0.6861 Remote Similarity NPC470142
0.6763 Remote Similarity NPC313504
0.6589 Remote Similarity NPC273327
0.6562 Remote Similarity NPC124276
0.6384 Remote Similarity NPC201900
0.6289 Remote Similarity NPC282531
0.6229 Remote Similarity NPC477118
0.6218 Remote Similarity NPC197068
0.6193 Remote Similarity NPC477120
0.6163 Remote Similarity NPC477119
0.6026 Remote Similarity NPC8590
0.6 Remote Similarity NPC313547
0.5986 Remote Similarity NPC68938
0.5952 Remote Similarity NPC472790
0.595 Remote Similarity NPC237936
0.5933 Remote Similarity NPC246193
0.5924 Remote Similarity NPC315642
0.5924 Remote Similarity NPC74306
0.5882 Remote Similarity NPC476099
0.5875 Remote Similarity NPC42483
0.5851 Remote Similarity NPC54537
0.5838 Remote Similarity NPC238945
0.5825 Remote Similarity NPC477417
0.5825 Remote Similarity NPC477419
0.5821 Remote Similarity NPC293163
0.5793 Remote Similarity NPC252603
0.5793 Remote Similarity NPC473646
0.5764 Remote Similarity NPC278549
0.5748 Remote Similarity NPC190949
0.5735 Remote Similarity NPC323244
0.5734 Remote Similarity NPC148385
0.5704 Remote Similarity NPC41958
0.5693 Remote Similarity NPC59314
0.5685 Remote Similarity NPC282247
0.5682 Remote Similarity NPC51000
0.5677 Remote Similarity NPC262926
0.567 Remote Similarity NPC476525
0.5641 Remote Similarity NPC320818
0.5641 Remote Similarity NPC61198
0.5629 Remote Similarity NPC144223
0.5625 Remote Similarity NPC63433
0.5625 Remote Similarity NPC328924

  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 NPC25465 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
0.9141 High Similarity NPD9133 Approved
0.9141 High Similarity NPD9628 Approved
0.8797 High Similarity NPD9183 Clinical (unspecified phase)
0.8667 High Similarity NPD9627 Approved
0.8519 High Similarity NPD1451 Approved
0.8438 Intermediate Similarity NPD300 Approved
0.837 Intermediate Similarity NPD875 Clinical (unspecified phase)
0.7891 Intermediate Similarity NPD3697 Discontinued
0.7801 Intermediate Similarity NPD568 Approved
0.7801 Intermediate Similarity NPD567 Approved
0.7801 Intermediate Similarity NPD566 Approved
0.777 Intermediate Similarity NPD2604 Approved
0.7755 Intermediate Similarity NPD2180 Approved
0.7687 Intermediate Similarity NPD1731 Clinical (unspecified phase)
0.7656 Intermediate Similarity NPD9132 Discontinued
0.7623 Intermediate Similarity NPD8862 Approved
0.7623 Intermediate Similarity NPD8859 Approved
0.7623 Intermediate Similarity NPD8861 Approved
0.7566 Intermediate Similarity NPD3130 Discontinued
0.7552 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD1389 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD1388 Phase 1
0.7333 Intermediate Similarity NPD1390 Phase 1
0.731 Intermediate Similarity NPD3706 Clinical (unspecified phase)
0.725 Intermediate Similarity NPD3108 Clinical (unspecified phase)
0.7125 Intermediate Similarity NPD3105 Discontinued
0.7115 Intermediate Similarity NPD5768 Phase 2
0.7 Intermediate Similarity NPD1807 Clinical (unspecified phase)
0.695 Remote Similarity NPD9081 Clinical (unspecified phase)
0.6828 Remote Similarity NPD576 Discontinued
0.6364 Remote Similarity NPD7465 Suspended
0.6266 Remote Similarity NPD3708 Phase 2
0.6214 Remote Similarity NPD1368 Approved
0.6213 Remote Similarity NPD3347 Clinical (unspecified phase)
0.6209 Remote Similarity NPD1249 Clinical (unspecified phase)
0.619 Remote Similarity NPD8261 Discontinued
0.6162 Remote Similarity NPD3497 Clinical (unspecified phase)
0.6149 Remote Similarity NPD1027 Approved
0.6149 Remote Similarity NPD1030 Approved
0.6149 Remote Similarity NPD1029 Clinical (unspecified phase)
0.6133 Remote Similarity NPD8641 Approved
0.6078 Remote Similarity NPD1808 Phase 1
0.6074 Remote Similarity NPD1303 Phase 1
0.6045 Remote Similarity NPD340 Approved
0.6045 Remote Similarity NPD341 Approved
0.6026 Remote Similarity NPD209 Clinical (unspecified phase)
0.6014 Remote Similarity NPD8955 Approved
0.6014 Remote Similarity NPD8954 Approved
0.6 Remote Similarity NPD1290 Phase 2
0.6 Remote Similarity NPD8271 Discontinued
0.5988 Remote Similarity NPD1037 Clinical (unspecified phase)
0.5976 Remote Similarity NPD695 Discontinued
0.595 Remote Similarity NPD8185 Discontinued
0.595 Remote Similarity NPD8186 Phase 1
0.5948 Remote Similarity NPD1121 Approved
0.5948 Remote Similarity NPD1120 Approved
0.5926 Remote Similarity NPD7842 Phase 2
0.5924 Remote Similarity NPD1117 Clinical (unspecified phase)
0.5924 Remote Similarity NPD582 Approved
0.5894 Remote Similarity NPD9650 Phase 3
0.589 Remote Similarity NPD536 Clinical (unspecified phase)
0.5879 Remote Similarity NPD459 Clinical (unspecified phase)
0.5875 Remote Similarity NPD9724 Phase 1
0.587 Remote Similarity NPD978 Clinical (unspecified phase)
0.587 Remote Similarity NPD8113 Phase 2
0.5868 Remote Similarity NPD1335 Approved
0.5846 Remote Similarity NPD9210 Phase 2
0.5843 Remote Similarity NPD3586 Phase 2
0.5833 Remote Similarity NPD1042 Clinical (unspecified phase)
0.5833 Remote Similarity NPD9360 Approved
0.5815 Remote Similarity NPD460 Discontinued
0.5811 Remote Similarity NPD579 Clinical (unspecified phase)
0.5808 Remote Similarity NPD276 Clinical (unspecified phase)
0.5801 Remote Similarity NPD2009 Clinical (unspecified phase)
0.5796 Remote Similarity NPD1118 Discontinued
0.5793 Remote Similarity NPD76 Approved
0.5793 Remote Similarity NPD9288 Approved
0.5793 Remote Similarity NPD9292 Approved
0.5793 Remote Similarity NPD9289 Approved
0.5767 Remote Similarity NPD8629 Discontinued
0.5759 Remote Similarity NPD1430 Approved
0.5759 Remote Similarity NPD1431 Approved
0.5749 Remote Similarity NPD3405 Phase 3
0.5735 Remote Similarity NPD8292 Phase 2
0.5734 Remote Similarity NPD757 Phase 3
0.5733 Remote Similarity NPD515 Phase 1
0.5723 Remote Similarity NPD2618 Phase 1
0.57 Remote Similarity NPD8119 Discontinued
0.5695 Remote Similarity NPD870 Clinical (unspecified phase)
0.5693 Remote Similarity NPD8837 Clinical (unspecified phase)
0.5682 Remote Similarity NPD8838 Approved
0.5677 Remote Similarity NPD194 Clinical (unspecified phase)
0.5674 Remote Similarity NPD1327 Discontinued
0.5649 Remote Similarity NPD545 Clinical (unspecified phase)
0.5649 Remote Similarity NPD547 Clinical (unspecified phase)
0.5648 Remote Similarity NPD2008 Discontinued
0.5644 Remote Similarity NPD775 Approved
0.5641 Remote Similarity NPD252 Clinical (unspecified phase)
0.5625 Remote Similarity NPD2179 Discontinued
0.5621 Remote Similarity NPD9632 Phase 3
0.5619 Remote Similarity NPD7834 Approved
0.5619 Remote Similarity NPD8410 Clinical (unspecified phase)
0.5616 Remote Similarity NPD237 Clinical (unspecified phase)
0.5612 Remote Similarity NPD5072 Discontinued
0.5606 Remote Similarity NPD4341 Clinical (unspecified phase)
0.5604 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5604 Remote Similarity NPD7245 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