Structure

Physi-Chem Properties

Molecular Weight:  140.06
Volume:  135.441
LogP:  -1.245
LogD:  -1.045
LogS:  -0.221
# Rotatable Bonds:  3
TPSA:  65.98
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.639
Synthetic Accessibility Score:  2.693
Fsp3:  0.333
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:  -5.381
MDCK Permeability:  3.0660883112432202e-06
Pgp-inhibitor:  0.002
Pgp-substrate:  0.075
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.041

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.165
Plasma Protein Binding (PPB):  17.997718811035156%
Volume Distribution (VD):  0.315
Pgp-substrate:  77.5254135131836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.135
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.038
CYP3A4-inhibitor:  0.077
CYP3A4-substrate:  0.054

ADMET: Excretion

Clearance (CL):  7.838
Half-life (T1/2):  0.929

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.154
Drug-inuced Liver Injury (DILI):  0.43
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.047
Maximum Recommended Daily Dose:  0.096
Skin Sensitization:  0.761
Carcinogencity:  0.022
Eye Corrosion:  0.028
Eye Irritation:  0.95
Respiratory Toxicity:  0.054

Download Data

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

  Natural Product: NPC235501

Natural Product ID:  NPC235501
Common Name*:   3-(1H-Imidazol-5-Yl)Propanoic Acid
IUPAC Name:   3-(1H-imidazol-5-yl)propanoic acid
Synonyms:  
Standard InCHIKey:  ZCKYOWGFRHAZIQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H8N2O2/c9-6(10)2-1-5-3-7-4-8-5/h3-4H,1-2H2,(H,7,8)(H,9,10)
SMILES:  OC(=O)CCc1cnc[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL84253
PubChem CID:   70630
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
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30607 Coprinus atramentarius Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae 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
NPT4430 Individual Protein Histidine decarboxylase Rattus norvegicus Inhibition = 9.0 % PMID[558800]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus IC50 = 290000.0 nM PMID[558797]
NPT2 Others Unspecified Ratio pIC50 >= 44.0 n.a. PMID[558798]
NPT2 Others Unspecified Ratio pIC50 = 29.0 n.a. PMID[558798]
NPT2 Others Unspecified Ratio pIC50 = 4.0 n.a. PMID[558798]
NPT813 Individual Protein GABA transporter 1 Mus musculus Activity = 61.7 % PMID[558798]
NPT815 Individual Protein GABA transporter 3 Mus musculus IC50 = 645654.23 nM PMID[558798]
NPT816 Individual Protein GABA transporter 4 Mus musculus IC50 = 22908.68 nM PMID[558798]
NPT2 Others Unspecified IC50 = 81283.05 nM PMID[558798]
NPT2 Others Unspecified IC50 = 3170.0 nM PMID[558799]

☑ 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 NPC235501 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
0.96 High Similarity NPC237812
0.96 High Similarity NPC18223
0.9512 High Similarity NPC25465
0.9375 High Similarity NPC286696
0.9375 High Similarity NPC185903
0.9091 High Similarity NPC174020
0.9023 High Similarity NPC327477
0.8984 High Similarity NPC126634
0.872 High Similarity NPC15566
0.8712 High Similarity NPC210947
0.8583 High Similarity NPC180462
0.8462 Intermediate Similarity NPC470138
0.8209 Intermediate Similarity NPC470140
0.8125 Intermediate Similarity NPC60537
0.8029 Intermediate Similarity NPC470139
0.792 Intermediate Similarity NPC327613
0.7623 Intermediate Similarity NPC111132
0.75 Intermediate Similarity NPC155498
0.7239 Intermediate Similarity NPC470142
0.7194 Intermediate Similarity NPC243319
0.719 Intermediate Similarity NPC9639
0.7133 Intermediate Similarity NPC470141
0.704 Intermediate Similarity NPC187191
0.704 Intermediate Similarity NPC326248
0.685 Remote Similarity NPC273327
0.6763 Remote Similarity NPC313504
0.6497 Remote Similarity NPC282531
0.6384 Remote Similarity NPC201900
0.6259 Remote Similarity NPC246193
0.6258 Remote Similarity NPC124276
0.6234 Remote Similarity NPC8590
0.6232 Remote Similarity NPC313547
0.6183 Remote Similarity NPC293163
0.6136 Remote Similarity NPC477118
0.6115 Remote Similarity NPC197068
0.6102 Remote Similarity NPC477120
0.6069 Remote Similarity NPC477119
0.6045 Remote Similarity NPC59314
0.6026 Remote Similarity NPC315642
0.6026 Remote Similarity NPC74306
0.5986 Remote Similarity NPC68938
0.5952 Remote Similarity NPC472790
0.595 Remote Similarity NPC237936
0.5946 Remote Similarity NPC144223
0.5929 Remote Similarity NPC41958
0.5928 Remote Similarity NPC282247
0.5918 Remote Similarity NPC238945
0.5891 Remote Similarity NPC323244
0.5874 Remote Similarity NPC278549
0.5851 Remote Similarity NPC54537
0.5845 Remote Similarity NPC63433
0.5793 Remote Similarity NPC473646
0.5779 Remote Similarity NPC262926
0.5777 Remote Similarity NPC328924
0.5776 Remote Similarity NPC42483
0.5766 Remote Similarity NPC476099
0.5748 Remote Similarity NPC190949
0.5746 Remote Similarity NPC62749
0.5744 Remote Similarity NPC477419
0.5744 Remote Similarity NPC477417
0.5742 Remote Similarity NPC61198
0.5685 Remote Similarity NPC252603
0.5682 Remote Similarity NPC51000
0.567 Remote Similarity NPC476524
0.5663 Remote Similarity NPC54981
0.5655 Remote Similarity NPC240084
0.5655 Remote Similarity NPC33229
0.5649 Remote Similarity NPC57279
0.5641 Remote Similarity NPC320818
0.5625 Remote Similarity NPC148385
0.5622 Remote Similarity NPC210123
0.5604 Remote Similarity NPC69843
0.5602 Remote Similarity NPC207633

  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 NPC235501 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
0.96 High Similarity NPD9133 Approved
0.9231 High Similarity NPD9183 Clinical (unspecified phase)
0.9141 High Similarity NPD9628 Approved
0.8939 High Similarity NPD1451 Approved
0.888 High Similarity NPD300 Approved
0.8667 High Similarity NPD9627 Approved
0.8647 High Similarity NPD875 Clinical (unspecified phase)
0.8125 Intermediate Similarity NPD2180 Approved
0.8056 Intermediate Similarity NPD1731 Clinical (unspecified phase)
0.8014 Intermediate Similarity NPD2604 Approved
0.8014 Intermediate Similarity NPD3697 Discontinued
0.7801 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.78 Intermediate Similarity NPD3130 Discontinued
0.7656 Intermediate Similarity NPD9132 Discontinued
0.7623 Intermediate Similarity NPD8862 Approved
0.7623 Intermediate Similarity NPD8859 Approved
0.7623 Intermediate Similarity NPD8861 Approved
0.7468 Intermediate Similarity NPD3108 Clinical (unspecified phase)
0.7431 Intermediate Similarity NPD568 Approved
0.7431 Intermediate Similarity NPD567 Approved
0.7431 Intermediate Similarity NPD566 Approved
0.7342 Intermediate Similarity NPD3105 Discontinued
0.731 Intermediate Similarity NPD3706 Clinical (unspecified phase)
0.7226 Intermediate Similarity NPD5768 Phase 2
0.7206 Intermediate Similarity NPD1389 Clinical (unspecified phase)
0.7206 Intermediate Similarity NPD1388 Phase 1
0.7206 Intermediate Similarity NPD1390 Phase 1
0.7194 Intermediate Similarity NPD9081 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD1807 Clinical (unspecified phase)
0.6712 Remote Similarity NPD576 Discontinued
0.6364 Remote Similarity NPD7465 Suspended
0.6364 Remote Similarity NPD8261 Discontinued
0.6339 Remote Similarity NPD3497 Clinical (unspecified phase)
0.6313 Remote Similarity NPD8641 Approved
0.6272 Remote Similarity NPD1037 Clinical (unspecified phase)
0.6266 Remote Similarity NPD3708 Phase 2
0.6209 Remote Similarity NPD1249 Clinical (unspecified phase)
0.6145 Remote Similarity NPD459 Clinical (unspecified phase)
0.6133 Remote Similarity NPD209 Clinical (unspecified phase)
0.6129 Remote Similarity NPD1117 Clinical (unspecified phase)
0.6118 Remote Similarity NPD3347 Clinical (unspecified phase)
0.6098 Remote Similarity NPD276 Clinical (unspecified phase)
0.6078 Remote Similarity NPD1808 Phase 1
0.6061 Remote Similarity NPD1335 Approved
0.6056 Remote Similarity NPD9360 Approved
0.6049 Remote Similarity NPD1027 Approved
0.6049 Remote Similarity NPD1029 Clinical (unspecified phase)
0.6049 Remote Similarity NPD1030 Approved
0.6045 Remote Similarity NPD8837 Clinical (unspecified phase)
0.6044 Remote Similarity NPD8113 Phase 2
0.6026 Remote Similarity NPD582 Approved
0.6 Remote Similarity NPD8271 Discontinued
0.5988 Remote Similarity NPD536 Clinical (unspecified phase)
0.5976 Remote Similarity NPD695 Discontinued
0.5976 Remote Similarity NPD1303 Phase 1
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
0.5946 Remote Similarity NPD515 Phase 1
0.5926 Remote Similarity NPD7842 Phase 2
0.5926 Remote Similarity NPD340 Approved
0.5926 Remote Similarity NPD341 Approved
0.5906 Remote Similarity NPD870 Clinical (unspecified phase)
0.5904 Remote Similarity NPD1290 Phase 2
0.5902 Remote Similarity NPD460 Discontinued
0.5899 Remote Similarity NPD8954 Approved
0.5899 Remote Similarity NPD8955 Approved
0.5897 Remote Similarity NPD1118 Discontinued
0.5891 Remote Similarity NPD8292 Phase 2
0.5874 Remote Similarity NPD1368 Approved
0.5866 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5866 Remote Similarity NPD7245 Approved
0.5855 Remote Similarity NPD547 Clinical (unspecified phase)
0.5855 Remote Similarity NPD545 Clinical (unspecified phase)
0.5851 Remote Similarity NPD8629 Discontinued
0.5845 Remote Similarity NPD757 Phase 3
0.5843 Remote Similarity NPD3405 Phase 3
0.5839 Remote Similarity NPD775 Approved
0.5833 Remote Similarity NPD237 Clinical (unspecified phase)
0.5801 Remote Similarity NPD2009 Clinical (unspecified phase)
0.5793 Remote Similarity NPD307 Approved
0.5779 Remote Similarity NPD194 Clinical (unspecified phase)
0.5776 Remote Similarity NPD9724 Phase 1
0.5761 Remote Similarity NPD996 Phase 2
0.5761 Remote Similarity NPD994 Phase 2
0.5759 Remote Similarity NPD1430 Approved
0.5759 Remote Similarity NPD1431 Approved
0.5754 Remote Similarity NPD2137 Approved
0.5754 Remote Similarity NPD2138 Approved
0.5742 Remote Similarity NPD252 Clinical (unspecified phase)
0.574 Remote Similarity NPD1042 Clinical (unspecified phase)
0.5725 Remote Similarity NPD9210 Phase 2
0.5724 Remote Similarity NPD9632 Phase 3
0.5723 Remote Similarity NPD2618 Phase 1
0.5705 Remote Similarity NPD579 Clinical (unspecified phase)
0.57 Remote Similarity NPD8119 Discontinued
0.5699 Remote Similarity NPD7834 Approved
0.5699 Remote Similarity NPD978 Clinical (unspecified phase)
0.5699 Remote Similarity NPD8410 Clinical (unspecified phase)
0.5695 Remote Similarity NPD1355 Clinical (unspecified phase)
0.5695 Remote Similarity NPD1354 Approved
0.5695 Remote Similarity NPD1356 Approved
0.5686 Remote Similarity NPD9650 Phase 3
0.5685 Remote Similarity NPD9292 Approved
0.5685 Remote Similarity NPD9289 Approved
0.5685 Remote Similarity NPD9288 Approved
0.5685 Remote Similarity NPD76 Approved
0.5682 Remote Similarity NPD8838 Approved
0.5672 Remote Similarity NPD245 Suspended
0.567 Remote Similarity NPD7981 Discontinued
0.5652 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5635 Remote Similarity NPD2457 Phase 2
0.5635 Remote Similarity NPD2456 Phase 2
0.5634 Remote Similarity NPD9375 Discontinued
0.5632 Remote Similarity NPD9582 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