Structure

Physi-Chem Properties

Molecular Weight:  211.07
Volume:  203.58
LogP:  3.231
LogD:  3.018
LogS:  -5.335
# Rotatable Bonds:  3
TPSA:  52.32
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.761
Synthetic Accessibility Score:  2.228
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.457
MDCK Permeability:  3.8196965761017054e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.963
Plasma Protein Binding (PPB):  87.2004165649414%
Volume Distribution (VD):  1.108
Pgp-substrate:  16.554275512695312%

ADMET: Metabolism

CYP1A2-inhibitor:  0.986
CYP1A2-substrate:  0.87
CYP2C19-inhibitor:  0.87
CYP2C19-substrate:  0.396
CYP2C9-inhibitor:  0.521
CYP2C9-substrate:  0.473
CYP2D6-inhibitor:  0.349
CYP2D6-substrate:  0.761
CYP3A4-inhibitor:  0.312
CYP3A4-substrate:  0.178

ADMET: Excretion

Clearance (CL):  8.487
Half-life (T1/2):  0.086

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.061
Drug-inuced Liver Injury (DILI):  0.165
AMES Toxicity:  0.079
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.191
Skin Sensitization:  0.426
Carcinogencity:  0.188
Eye Corrosion:  0.01
Eye Irritation:  0.518
Respiratory Toxicity:  0.238

Download Data

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

  Natural Product: NPC23908

Natural Product ID:  NPC23908
Common Name*:   Ethyl 2-Amino-5,6-Dihydro-4H-Cyclopenta[B]Thiophene-3-Carboxylate
IUPAC Name:   ethyl 2-amino-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxylate
Synonyms:  
Standard InCHIKey:  BOJXCJDYZJSPMZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H13NO2S/c1-2-13-10(12)8-6-4-3-5-7(6)14-9(8)11/h2-5,11H2,1H3
SMILES:  CCOC(=O)c1c(N)sc2c1CCC2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL341097
PubChem CID:   264105
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000097] Thiophenes
        • [CHEMONTID:0001936] Aminothiophenes
          • [CHEMONTID:0004004] 2-aminothiophenes
            • [CHEMONTID:0004005] 3,4,5-trisubstituted-2-aminothiophenes

*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
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. stem n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. flower n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. leaf n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. PMID[6387056]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26589 Artemisia annua L. Strain Asteraceae 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
NPT216 Individual Protein Adenosine A1 receptor Homo sapiens AE Score = 0.4 % PMID[524537]
NPT216 Individual Protein Adenosine A1 receptor Homo sapiens Inhibition = 58.0 % PMID[524537]

☑ 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 NPC23908 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
0.695 Remote Similarity NPC226794
0.6759 Remote Similarity NPC122235
0.649 Remote Similarity NPC173295
0.6207 Remote Similarity NPC130931
0.6154 Remote Similarity NPC319645
0.6053 Remote Similarity NPC477432
0.6043 Remote Similarity NPC265407
0.6043 Remote Similarity NPC83628
0.6015 Remote Similarity NPC276775
0.6015 Remote Similarity NPC92754
0.6015 Remote Similarity NPC249912
0.6 Remote Similarity NPC253476
0.597 Remote Similarity NPC78701
0.597 Remote Similarity NPC225060
0.597 Remote Similarity NPC35448
0.5926 Remote Similarity NPC146351
0.5912 Remote Similarity NPC89886
0.5906 Remote Similarity NPC26285
0.5903 Remote Similarity NPC32356
0.5882 Remote Similarity NPC70624
0.5865 Remote Similarity NPC130398
0.585 Remote Similarity NPC229353
0.5849 Remote Similarity NPC181527
0.5833 Remote Similarity NPC307651
0.5809 Remote Similarity NPC118343
0.5797 Remote Similarity NPC474365
0.5797 Remote Similarity NPC301943
0.5786 Remote Similarity NPC37622
0.5786 Remote Similarity NPC30594
0.5786 Remote Similarity NPC119271
0.5782 Remote Similarity NPC227660
0.5772 Remote Similarity NPC150323
0.5766 Remote Similarity NPC42211
0.5745 Remote Similarity NPC56493
0.5734 Remote Similarity NPC210089
0.5725 Remote Similarity NPC188895
0.5725 Remote Similarity NPC45613
0.5706 Remote Similarity NPC191310
0.5704 Remote Similarity NPC474364
0.5704 Remote Similarity NPC10251
0.5704 Remote Similarity NPC469636
0.5704 Remote Similarity NPC17417
0.5694 Remote Similarity NPC270699
0.5694 Remote Similarity NPC82899
0.5693 Remote Similarity NPC325497
0.5693 Remote Similarity NPC203925
0.5686 Remote Similarity NPC205946
0.5679 Remote Similarity NPC43477
0.5674 Remote Similarity NPC475086
0.5664 Remote Similarity NPC196246
0.5664 Remote Similarity NPC214067
0.5664 Remote Similarity NPC174099
0.5664 Remote Similarity NPC93084
0.5664 Remote Similarity NPC251854
0.5655 Remote Similarity NPC128368
0.5646 Remote Similarity NPC149691
0.5643 Remote Similarity NPC31786
0.5633 Remote Similarity NPC130655
0.5625 Remote Similarity NPC474157
0.5625 Remote Similarity NPC167504
0.5625 Remote Similarity NPC305912
0.5625 Remote Similarity NPC1082
0.5625 Remote Similarity NPC260818
0.5603 Remote Similarity NPC209632
0.5603 Remote Similarity NPC269457
0.5602 Remote Similarity NPC259678

  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 NPC23908 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
0.7667 Intermediate Similarity NPD2512 Phase 3
0.6621 Remote Similarity NPD9567 Approved
0.6621 Remote Similarity NPD552 Approved
0.6621 Remote Similarity NPD553 Approved
0.6516 Remote Similarity NPD1116 Approved
0.6516 Remote Similarity NPD1113 Approved
0.6424 Remote Similarity NPD1588 Clinical (unspecified phase)
0.634 Remote Similarity NPD684 Approved
0.634 Remote Similarity NPD686 Approved
0.6328 Remote Similarity NPD6891 Phase 2
0.6258 Remote Similarity NPD5580 Discontinued
0.6258 Remote Similarity NPD3170 Approved
0.6242 Remote Similarity NPD6414 Clinical (unspecified phase)
0.6242 Remote Similarity NPD685 Approved
0.6185 Remote Similarity NPD3948 Discontinued
0.6184 Remote Similarity NPD3502 Discovery
0.6154 Remote Similarity NPD1109 Approved
0.6154 Remote Similarity NPD1110 Approved
0.6133 Remote Similarity NPD6659 Phase 2
0.6084 Remote Similarity NPD2672 Discontinued
0.6074 Remote Similarity NPD2737 Clinical (unspecified phase)
0.6014 Remote Similarity NPD1246 Approved
0.6 Remote Similarity NPD6384 Phase 2
0.6 Remote Similarity NPD6383 Clinical (unspecified phase)
0.5987 Remote Similarity NPD2670 Approved
0.5986 Remote Similarity NPD1279 Clinical (unspecified phase)
0.5957 Remote Similarity NPD2181 Clinical (unspecified phase)
0.5949 Remote Similarity NPD1626 Approved
0.5918 Remote Similarity NPD1245 Approved
0.5906 Remote Similarity NPD518 Clinical (unspecified phase)
0.5893 Remote Similarity NPD2836 Approved
0.5886 Remote Similarity NPD1194 Discontinued
0.5871 Remote Similarity NPD9471 Clinical (unspecified phase)
0.5867 Remote Similarity NPD1877 Discontinued
0.5854 Remote Similarity NPD1801 Approved
0.5854 Remote Similarity NPD1340 Discontinued
0.5854 Remote Similarity NPD1802 Approved
0.5818 Remote Similarity NPD7528 Approved
0.5809 Remote Similarity NPD1238 Approved
0.5804 Remote Similarity NPD9508 Approved
0.5802 Remote Similarity NPD1625 Approved
0.5789 Remote Similarity NPD1574 Approved
0.5782 Remote Similarity NPD2347 Approved
0.5772 Remote Similarity NPD9272 Approved
0.5764 Remote Similarity NPD5277 Phase 2
0.5733 Remote Similarity NPD9692 Approved
0.5733 Remote Similarity NPD9693 Approved
0.5724 Remote Similarity NPD661 Approved
0.5724 Remote Similarity NPD657 Approved
0.5724 Remote Similarity NPD655 Approved
0.5724 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5724 Remote Similarity NPD660 Approved
0.5714 Remote Similarity NPD2034 Discontinued
0.5714 Remote Similarity NPD701 Approved
0.5714 Remote Similarity NPD698 Approved
0.5704 Remote Similarity NPD2182 Approved
0.5686 Remote Similarity NPD2199 Approved
0.5686 Remote Similarity NPD2198 Approved
0.5677 Remote Similarity NPD659 Approved
0.5677 Remote Similarity NPD662 Approved
0.5677 Remote Similarity NPD658 Approved
0.5677 Remote Similarity NPD663 Approved
0.5677 Remote Similarity NPD656 Approved
0.5658 Remote Similarity NPD4232 Approved
0.5657 Remote Similarity NPD3861 Approved
0.5657 Remote Similarity NPD3862 Approved
0.565 Remote Similarity NPD4679 Discontinued
0.5647 Remote Similarity NPD1092 Approved
0.5647 Remote Similarity NPD1093 Approved
0.5647 Remote Similarity NPD3684 Discontinued
0.5644 Remote Similarity NPD1189 Approved
0.5643 Remote Similarity NPD164 Approved
0.564 Remote Similarity NPD3388 Phase 1
0.5629 Remote Similarity NPD4888 Discontinued
0.5621 Remote Similarity NPD182 Clinical (unspecified phase)
0.5617 Remote Similarity NPD7137 Phase 2
0.5611 Remote Similarity NPD3449 Discontinued
0.56 Remote Similarity NPD446 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