Structure

Physi-Chem Properties

Molecular Weight:  230.04
Volume:  239.846
LogP:  3.251
LogD:  2.323
LogS:  -3.807
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.701
Synthetic Accessibility Score:  4.214
Fsp3:  0.231
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.338
MDCK Permeability:  8.91653835424222e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.95
20% Bioavailability (F20%):  0.853
30% Bioavailability (F30%):  0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  101.30036926269531%
Volume Distribution (VD):  1.424
Pgp-substrate:  1.9957233667373657%

ADMET: Metabolism

CYP1A2-inhibitor:  0.921
CYP1A2-substrate:  0.131
CYP2C19-inhibitor:  0.885
CYP2C19-substrate:  0.419
CYP2C9-inhibitor:  0.92
CYP2C9-substrate:  0.919
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.469
CYP3A4-inhibitor:  0.714
CYP3A4-substrate:  0.229

ADMET: Excretion

Clearance (CL):  8.05
Half-life (T1/2):  0.07

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.454
Drug-inuced Liver Injury (DILI):  0.985
AMES Toxicity:  0.913
Rat Oral Acute Toxicity:  0.851
Maximum Recommended Daily Dose:  0.946
Skin Sensitization:  0.942
Carcinogencity:  0.703
Eye Corrosion:  0.925
Eye Irritation:  0.985
Respiratory Toxicity:  0.9

Download Data

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

  Natural Product: NPC472169

Natural Product ID:  NPC472169
Common Name*:   4-(5-Penta-1,3-Diynylthiophen-2-Yl)But-3-Yne-1,2-Diol
IUPAC Name:   4-(5-penta-1,3-diynylthiophen-2-yl)but-3-yne-1,2-diol
Synonyms:  
Standard InCHIKey:  MZCFHXFKOQBSQU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H10O2S/c1-2-3-4-5-12-8-9-13(16-12)7-6-11(15)10-14/h8-9,11,14-15H,10H2,1H3
SMILES:  CC#CC#Cc1ccc(s1)C#CC(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3343899
PubChem CID:   25014552
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000097] Thiophenes
        • [CHEMONTID:0003481] 2,5-disubstituted thiophenes

*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 = 2740.0 nM PMID[570817]

☑ 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 NPC472169 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
0.9351 High Similarity NPC299367
0.8556 High Similarity NPC474934
0.8182 Intermediate Similarity NPC2751
0.7835 Intermediate Similarity NPC472170
0.775 Intermediate Similarity NPC105991
0.7629 Intermediate Similarity NPC475115
0.7045 Intermediate Similarity NPC8981
0.699 Remote Similarity NPC475086
0.6848 Remote Similarity NPC470794
0.6739 Remote Similarity NPC307163
0.6602 Remote Similarity NPC173019
0.6598 Remote Similarity NPC166487
0.6559 Remote Similarity NPC471895
0.6512 Remote Similarity NPC470795
0.6413 Remote Similarity NPC195713
0.64 Remote Similarity NPC300455
0.6275 Remote Similarity NPC175376
0.625 Remote Similarity NPC470796
0.619 Remote Similarity NPC22627
0.617 Remote Similarity NPC471376
0.6132 Remote Similarity NPC472171
0.61 Remote Similarity NPC470797
0.6075 Remote Similarity NPC472172
0.6053 Remote Similarity NPC32356
0.6036 Remote Similarity NPC190955
0.602 Remote Similarity NPC148231
0.5981 Remote Similarity NPC24122
0.5772 Remote Similarity NPC475082
0.5701 Remote Similarity NPC120203
0.5625 Remote Similarity NPC469894

  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 NPC472169 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
0.6226 Remote Similarity NPD744 Clinical (unspecified phase)
0.6111 Remote Similarity NPD745 Clinical (unspecified phase)
0.6068 Remote Similarity NPD446 Clinical (unspecified phase)
0.6055 Remote Similarity NPD183 Approved
0.6036 Remote Similarity NPD5278 Discontinued
0.5913 Remote Similarity NPD1246 Approved
0.5862 Remote Similarity NPD1944 Phase 2
0.5826 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5736 Remote Similarity NPD2202 Clinical (unspecified phase)
0.5703 Remote Similarity NPD4404 Approved
0.5667 Remote Similarity NPD1245 Approved
0.5649 Remote Similarity NPD5886 Approved
0.5649 Remote Similarity NPD41 Approved
0.5607 Remote Similarity NPD1672 Phase 2
0.5603 Remote Similarity NPD1279 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