Structure

Physi-Chem Properties

Molecular Weight:  292.01
Volume:  273.529
LogP:  5.358
LogD:  3.433
LogS:  -6.799
# Rotatable Bonds:  4
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.629
Synthetic Accessibility Score:  2.454
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.186
MDCK Permeability:  1.1887209439009894e-05
Pgp-inhibitor:  0.023
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.969
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.018
Plasma Protein Binding (PPB):  100.5299301147461%
Volume Distribution (VD):  1.792
Pgp-substrate:  1.2976462841033936%

ADMET: Metabolism

CYP1A2-inhibitor:  0.992
CYP1A2-substrate:  0.888
CYP2C19-inhibitor:  0.919
CYP2C19-substrate:  0.138
CYP2C9-inhibitor:  0.716
CYP2C9-substrate:  0.401
CYP2D6-inhibitor:  0.891
CYP2D6-substrate:  0.898
CYP3A4-inhibitor:  0.95
CYP3A4-substrate:  0.737

ADMET: Excretion

Clearance (CL):  1.702
Half-life (T1/2):  0.003

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.888
Drug-inuced Liver Injury (DILI):  0.884
AMES Toxicity:  0.494
Rat Oral Acute Toxicity:  0.258
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.112
Carcinogencity:  0.299
Eye Corrosion:  0.006
Eye Irritation:  0.596
Respiratory Toxicity:  0.577

Download Data

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

  Natural Product: NPC472171

Natural Product ID:  NPC472171
Common Name*:   BUCGRKJUXCTDSV-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BUCGRKJUXCTDSV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H12OS3/c1-15-9-10-4-5-13(17-10)14-7-6-12(18-14)11-3-2-8-16-11/h2-8H,9H2,1H3
SMILES:  COCC1=CC=C(S1)C2=CC=C(S2)C3=CC=CS3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3343902
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002021] Bi- and oligothiophenes

*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
NPO33375 eclipata prostrata Species n.a. n.a. aerial parts n.a. n.a. PMID[25443644]

☑ 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
NPT1592 Individual Protein Dipeptidyl peptidase IV Homo sapiens IC50 = 2390.0 nM PMID[494495]

☑ 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 NPC472171 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
0.9895 High Similarity NPC472172
0.899 High Similarity NPC173019
0.8692 High Similarity NPC221877
0.7872 Intermediate Similarity NPC195713
0.7857 Intermediate Similarity NPC32356
0.7757 Intermediate Similarity NPC472170
0.7353 Intermediate Similarity NPC2751
0.7297 Intermediate Similarity NPC475086
0.7248 Intermediate Similarity NPC24122
0.7216 Intermediate Similarity NPC8981
0.7196 Intermediate Similarity NPC474934
0.6789 Remote Similarity NPC175376
0.6786 Remote Similarity NPC475115
0.6436 Remote Similarity NPC299367
0.6392 Remote Similarity NPC105991
0.6231 Remote Similarity NPC475082
0.6132 Remote Similarity NPC472169
0.6095 Remote Similarity NPC165212
0.6038 Remote Similarity NPC106313
0.6036 Remote Similarity NPC166487
0.6036 Remote Similarity NPC185501
0.5984 Remote Similarity NPC190955
0.5981 Remote Similarity NPC471895
0.5981 Remote Similarity NPC307163
0.5963 Remote Similarity NPC148231
0.5877 Remote Similarity NPC300455
0.5872 Remote Similarity NPC58616
0.5856 Remote Similarity NPC304760
0.5785 Remote Similarity NPC472919
0.578 Remote Similarity NPC470794
0.5766 Remote Similarity NPC89377
0.5686 Remote Similarity NPC470796
0.5664 Remote Similarity NPC220893
0.5664 Remote Similarity NPC173443
0.5612 Remote Similarity NPC22627

  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 NPC472171 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
0.7083 Intermediate Similarity NPD446 Clinical (unspecified phase)
0.6855 Remote Similarity NPD1877 Discontinued
0.65 Remote Similarity NPD1279 Clinical (unspecified phase)
0.6283 Remote Similarity NPD1672 Phase 2
0.6269 Remote Similarity NPD4404 Approved
0.6204 Remote Similarity NPD41 Approved
0.6204 Remote Similarity NPD5886 Approved
0.6179 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6164 Remote Similarity NPD6813 Clinical (unspecified phase)
0.6116 Remote Similarity NPD5278 Discontinued
0.6058 Remote Similarity NPD2202 Clinical (unspecified phase)
0.5918 Remote Similarity NPD2901 Approved
0.5918 Remote Similarity NPD2900 Approved
0.5891 Remote Similarity NPD1245 Approved
0.5887 Remote Similarity NPD2862 Discontinued
0.5873 Remote Similarity NPD1246 Approved
0.5859 Remote Similarity NPD2347 Approved
0.5817 Remote Similarity NPD3493 Approved
0.5817 Remote Similarity NPD3492 Approved
0.5817 Remote Similarity NPD3494 Approved
0.5786 Remote Similarity NPD442 Discontinued
0.5735 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1295 Clinical (unspecified phase)
0.5664 Remote Similarity NPD7137 Phase 2
0.5639 Remote Similarity NPD4480 Approved
0.5638 Remote Similarity NPD6890 Discontinued

  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