Structure

Physi-Chem Properties

Molecular Weight:  255.12
Volume:  247.861
LogP:  0.122
LogD:  -0.231
LogS:  -0.68
# Rotatable Bonds:  8
TPSA:  82.45
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.763
Synthetic Accessibility Score:  2.816
Fsp3:  0.545
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.321
MDCK Permeability:  2.2525649910676293e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.102
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.534
Plasma Protein Binding (PPB):  12.74757194519043%
Volume Distribution (VD):  0.812
Pgp-substrate:  84.80774688720703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.101
CYP1A2-substrate:  0.717
CYP2C19-inhibitor:  0.177
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.074
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.237
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.217

ADMET: Excretion

Clearance (CL):  7.361
Half-life (T1/2):  0.927

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.562
Drug-inuced Liver Injury (DILI):  0.859
AMES Toxicity:  0.042
Rat Oral Acute Toxicity:  0.11
Maximum Recommended Daily Dose:  0.133
Skin Sensitization:  0.114
Carcinogencity:  0.136
Eye Corrosion:  0.003
Eye Irritation:  0.019
Respiratory Toxicity:  0.045

Download Data

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

  Natural Product: NPC470139

Natural Product ID:  NPC470139
Common Name*:   Methyl 2-(Ethoxycarbonylamino)-3-(1-Methylimidazol-4-Yl)Propanoate
IUPAC Name:   methyl 2-(ethoxycarbonylamino)-3-(1-methylimidazol-4-yl)propanoate
Synonyms:  
Standard InCHIKey:  YWUXMLPRMREDKJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H17N3O4/c1-4-18-11(16)13-9(10(15)17-3)5-8-6-14(2)7-12-8/h6-7,9H,4-5H2,1-3H3,(H,13,16)
SMILES:  CCOC(=O)NC(CC1=CN(C=N1)C)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1780250
PubChem CID:   54585577
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004311] Histidine 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 = 29300.0 nM PMID[558387]

☑ 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 NPC470139 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
0.9764 High Similarity NPC470140
0.8955 High Similarity NPC210947
0.8939 High Similarity NPC126634
0.8855 High Similarity NPC470138
0.8478 Intermediate Similarity NPC286696
0.8394 Intermediate Similarity NPC237812
0.8394 Intermediate Similarity NPC18223
0.8345 Intermediate Similarity NPC185903
0.8261 Intermediate Similarity NPC470141
0.8182 Intermediate Similarity NPC327477
0.8162 Intermediate Similarity NPC25465
0.8029 Intermediate Similarity NPC235501
0.7632 Intermediate Similarity NPC60537
0.763 Intermediate Similarity NPC470142
0.7619 Intermediate Similarity NPC174020
0.7609 Intermediate Similarity NPC180462
0.7 Intermediate Similarity NPC273327
0.6972 Remote Similarity NPC15566
0.6794 Remote Similarity NPC326248
0.6794 Remote Similarity NPC187191
0.678 Remote Similarity NPC313504
0.6687 Remote Similarity NPC124276
0.6619 Remote Similarity NPC327613
0.6471 Remote Similarity NPC155498
0.6369 Remote Similarity NPC74306
0.6369 Remote Similarity NPC315642
0.6324 Remote Similarity NPC111132
0.6223 Remote Similarity NPC54537
0.6121 Remote Similarity NPC207633
0.6082 Remote Similarity NPC472790
0.6054 Remote Similarity NPC201900
0.5987 Remote Similarity NPC320818
0.596 Remote Similarity NPC180493
0.5943 Remote Similarity NPC290959
0.5924 Remote Similarity NPC144474
0.5924 Remote Similarity NPC527
0.5924 Remote Similarity NPC133782
0.5902 Remote Similarity NPC477118
0.5871 Remote Similarity NPC238945
0.5871 Remote Similarity NPC243319
0.587 Remote Similarity NPC477120
0.5833 Remote Similarity NPC321052
0.5833 Remote Similarity NPC477119
0.5829 Remote Similarity NPC325906
0.5823 Remote Similarity NPC262926
0.5815 Remote Similarity NPC101676
0.5809 Remote Similarity NPC9639
0.5808 Remote Similarity NPC326694
0.5789 Remote Similarity NPC109322
0.5786 Remote Similarity NPC61198
0.5771 Remote Similarity NPC324484
0.574 Remote Similarity NPC473646
0.5723 Remote Similarity NPC309832
0.5714 Remote Similarity NPC30326
0.57 Remote Similarity NPC477417
0.57 Remote Similarity NPC477419
0.5694 Remote Similarity NPC323244
0.5663 Remote Similarity NPC189068
0.5647 Remote Similarity NPC282531
0.5629 Remote Similarity NPC219313
0.5616 Remote Similarity NPC47936
0.561 Remote Similarity NPC186619
0.5607 Remote Similarity NPC239737
0.5602 Remote Similarity NPC156461
0.5602 Remote Similarity NPC21448
0.5602 Remote Similarity NPC107374
0.5602 Remote Similarity NPC317746

  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 NPC470139 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
0.8394 Intermediate Similarity NPD9133 Approved
0.8261 Intermediate Similarity NPD9628 Approved
0.8227 Intermediate Similarity NPD1451 Approved
0.8214 Intermediate Similarity NPD875 Clinical (unspecified phase)
0.8042 Intermediate Similarity NPD568 Approved
0.8042 Intermediate Similarity NPD567 Approved
0.8042 Intermediate Similarity NPD566 Approved
0.7972 Intermediate Similarity NPD9183 Clinical (unspecified phase)
0.7862 Intermediate Similarity NPD9627 Approved
0.7763 Intermediate Similarity NPD3697 Discontinued
0.7647 Intermediate Similarity NPD2604 Approved
0.7632 Intermediate Similarity NPD2180 Approved
0.7566 Intermediate Similarity NPD1731 Clinical (unspecified phase)
0.7482 Intermediate Similarity NPD300 Approved
0.7452 Intermediate Similarity NPD3130 Discontinued
0.72 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.7152 Intermediate Similarity NPD3108 Clinical (unspecified phase)
0.703 Intermediate Similarity NPD3105 Discontinued
0.7019 Intermediate Similarity NPD5768 Phase 2
0.6959 Remote Similarity NPD576 Discontinued
0.6815 Remote Similarity NPD3708 Phase 2
0.6541 Remote Similarity NPD3497 Clinical (unspecified phase)
0.6525 Remote Similarity NPD9132 Discontinued
0.6429 Remote Similarity NPD1808 Phase 1
0.6395 Remote Similarity NPD1037 Clinical (unspecified phase)
0.6387 Remote Similarity NPD7465 Suspended
0.6369 Remote Similarity NPD582 Approved
0.6329 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6324 Remote Similarity NPD8859 Approved
0.6324 Remote Similarity NPD8862 Approved
0.6324 Remote Similarity NPD8861 Approved
0.6299 Remote Similarity NPD1120 Approved
0.6299 Remote Similarity NPD1121 Approved
0.6258 Remote Similarity NPD7842 Phase 2
0.6174 Remote Similarity NPD1388 Phase 1
0.6174 Remote Similarity NPD1389 Clinical (unspecified phase)
0.6174 Remote Similarity NPD1390 Phase 1
0.6167 Remote Similarity NPD1308 Approved
0.6129 Remote Similarity NPD1119 Phase 2
0.6118 Remote Similarity NPD1807 Clinical (unspecified phase)
0.6111 Remote Similarity NPD757 Phase 3
0.6101 Remote Similarity NPD1430 Approved
0.6101 Remote Similarity NPD1431 Approved
0.6101 Remote Similarity NPD2253 Discontinued
0.6056 Remote Similarity NPD2137 Approved
0.6056 Remote Similarity NPD2138 Approved
0.6051 Remote Similarity NPD8261 Discontinued
0.603 Remote Similarity NPD8271 Discontinued
0.6027 Remote Similarity NPD1368 Approved
0.6024 Remote Similarity NPD536 Clinical (unspecified phase)
0.6023 Remote Similarity NPD3083 Approved
0.5974 Remote Similarity NPD9632 Phase 3
0.596 Remote Similarity NPD78 Approved
0.596 Remote Similarity NPD9544 Approved
0.596 Remote Similarity NPD5679 Clinical (unspecified phase)
0.5935 Remote Similarity NPD9650 Phase 3
0.592 Remote Similarity NPD1623 Approved
0.5882 Remote Similarity NPD1775 Approved
0.5882 Remote Similarity NPD1085 Approved
0.5879 Remote Similarity NPD7557 Clinical (unspecified phase)
0.5879 Remote Similarity NPD4341 Clinical (unspecified phase)
0.5874 Remote Similarity NPD613 Phase 2
0.5871 Remote Similarity NPD9081 Clinical (unspecified phase)
0.5844 Remote Similarity NPD1127 Approved
0.5844 Remote Similarity NPD1128 Approved
0.5839 Remote Similarity NPD549 Approved
0.5829 Remote Similarity NPD1776 Approved
0.5829 Remote Similarity NPD1777 Approved
0.582 Remote Similarity NPD8641 Approved
0.5816 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5796 Remote Similarity NPD547 Clinical (unspecified phase)
0.5786 Remote Similarity NPD535 Approved
0.5786 Remote Similarity NPD252 Clinical (unspecified phase)
0.5783 Remote Similarity NPD775 Approved
0.5779 Remote Similarity NPD515 Phase 1
0.5772 Remote Similarity NPD578 Discontinued
0.5765 Remote Similarity NPD2662 Approved
0.5765 Remote Similarity NPD2660 Approved
0.5763 Remote Similarity NPD9582 Phase 3
0.5742 Remote Similarity NPD870 Clinical (unspecified phase)
0.574 Remote Similarity NPD9605 Phase 3
0.5735 Remote Similarity NPD8119 Discontinued
0.5732 Remote Similarity NPD174 Discontinued
0.5732 Remote Similarity NPD4240 Approved
0.5723 Remote Similarity NPD194 Clinical (unspecified phase)
0.5723 Remote Similarity NPD1335 Approved
0.5714 Remote Similarity NPD281 Approved
0.5696 Remote Similarity NPD545 Clinical (unspecified phase)
0.5694 Remote Similarity NPD8292 Phase 2
0.5692 Remote Similarity NPD2807 Discontinued
0.5664 Remote Similarity NPD9345 Clinical (unspecified phase)
0.5664 Remote Similarity NPD9371 Clinical (unspecified phase)
0.5664 Remote Similarity NPD9196 Phase 2
0.566 Remote Similarity NPD5340 Clinical (unspecified phase)
0.566 Remote Similarity NPD209 Clinical (unspecified phase)
0.5657 Remote Similarity NPD3839 Phase 2
0.5657 Remote Similarity NPD3840 Phase 2
0.5654 Remote Similarity NPD8113 Phase 2
0.565 Remote Similarity NPD5072 Discontinued
0.5645 Remote Similarity NPD7245 Approved
0.5645 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5641 Remote Similarity NPD4458 Phase 2
0.5641 Remote Similarity NPD8629 Discontinued
0.5641 Remote Similarity NPD4459 Clinical (unspecified phase)
0.5633 Remote Similarity NPD282 Approved
0.5629 Remote Similarity NPD307 Approved
0.5629 Remote Similarity NPD7531 Clinical (unspecified phase)
0.5628 Remote Similarity NPD3432 Approved
0.5615 Remote Similarity NPD3913 Clinical (unspecified phase)
0.5614 Remote Similarity NPD1369 Phase 2
0.5613 Remote Similarity NPD4812 Phase 1
0.5611 Remote Similarity NPD3347 Clinical (unspecified phase)
0.5607 Remote Similarity NPD2624 Phase 2
0.5607 Remote Similarity NPD2646 Discontinued
0.5602 Remote Similarity NPD250 Approved
0.5602 Remote Similarity NPD249 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