Structure

Physi-Chem Properties

Molecular Weight:  214.05
Volume:  231.055
LogP:  4.036
LogD:  2.604
LogS:  -4.982
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.707
Synthetic Accessibility Score:  3.506
Fsp3:  0.231
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:  -4.016
MDCK Permeability:  2.361116639804095e-05
Pgp-inhibitor:  0.138
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.571
20% Bioavailability (F20%):  0.912
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  100.95659637451172%
Volume Distribution (VD):  1.549
Pgp-substrate:  1.512873649597168%

ADMET: Metabolism

CYP1A2-inhibitor:  0.979
CYP1A2-substrate:  0.51
CYP2C19-inhibitor:  0.901
CYP2C19-substrate:  0.283
CYP2C9-inhibitor:  0.918
CYP2C9-substrate:  0.914
CYP2D6-inhibitor:  0.071
CYP2D6-substrate:  0.43
CYP3A4-inhibitor:  0.72
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  8.52
Half-life (T1/2):  0.047

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.081
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.716
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.26
Skin Sensitization:  0.959
Carcinogencity:  0.907
Eye Corrosion:  0.984
Eye Irritation:  0.994
Respiratory Toxicity:  0.774

Download Data

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

  Natural Product: NPC299367

Natural Product ID:  NPC299367
Common Name*:   4-(5-Penta-1,3-Diynylthiophen-2-Yl)But-3-Yn-1-Ol
IUPAC Name:   4-(5-penta-1,3-diynylthiophen-2-yl)but-3-yn-1-ol
Synonyms:  
Standard InCHIKey:  DGRYPUZVMYTRRW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H10OS/c1-2-3-4-7-12-9-10-13(15-12)8-5-6-11-14/h9-10,14H,6,11H2,1H3
SMILES:  CC#CC#Cc1ccc(C#CCCO)s1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2252904
PubChem CID:   14890287
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
NPO3608 Eleutherococcus giraldii Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3608 Eleutherococcus giraldii Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4597 Campanula lactiflora Species Campanulaceae 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
NPT637 Organism Fusarium oxysporum Fusarium oxysporum GI = 100.0 % PMID[502488]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides GI = 100.0 % PMID[502488]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana IC50 = 41000.0 nM PMID[502488]
NPT637 Organism Fusarium oxysporum Fusarium oxysporum IC50 = 20000.0 nM PMID[502488]
NPT852 Organism Phomopsis obscurans Phomopsis obscurans IC50 = 13500.0 nM PMID[502488]
NPT1095 Organism Plasmopara viticola Plasmopara viticola IC50 = 4000.0 nM PMID[502488]
NPT851 Organism Colletotrichum fragariae Colletotrichum fragariae IC50 = 12500.0 nM PMID[502488]
NPT1096 Organism Colletotrichum acutatum Colletotrichum acutatum IC50 = 19200.0 nM PMID[502488]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides IC50 = 6000.0 nM PMID[502488]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana IC50 = 29400.0 nM PMID[502488]
NPT637 Organism Fusarium oxysporum Fusarium oxysporum IC50 = 9500.0 nM PMID[502488]
NPT852 Organism Phomopsis obscurans Phomopsis obscurans IC50 = 2900.0 nM PMID[502488]
NPT1095 Organism Plasmopara viticola Plasmopara viticola IC50 < 1600.0 nM PMID[502488]
NPT851 Organism Colletotrichum fragariae Colletotrichum fragariae IC50 = 4400.0 nM PMID[502488]
NPT1096 Organism Colletotrichum acutatum Colletotrichum acutatum IC50 = 3500.0 nM PMID[502488]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides IC50 = 2600.0 nM PMID[502488]

☑ 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 NPC299367 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 NPC472169
0.8675 High Similarity NPC2751
0.8267 Intermediate Similarity NPC105991
0.8 Intermediate Similarity NPC474934
0.766 Intermediate Similarity NPC475115
0.747 Intermediate Similarity NPC8981
0.732 Intermediate Similarity NPC472170
0.7045 Intermediate Similarity NPC470794
0.6957 Remote Similarity NPC166487
0.6939 Remote Similarity NPC173019
0.6932 Remote Similarity NPC471895
0.6932 Remote Similarity NPC307163
0.6914 Remote Similarity NPC470795
0.6782 Remote Similarity NPC195713
0.6737 Remote Similarity NPC300455
0.6667 Remote Similarity NPC475086
0.6627 Remote Similarity NPC470796
0.6582 Remote Similarity NPC22627
0.6517 Remote Similarity NPC471376
0.6436 Remote Similarity NPC472171
0.6429 Remote Similarity NPC175376
0.6421 Remote Similarity NPC470797
0.6373 Remote Similarity NPC472172
0.6344 Remote Similarity NPC148231
0.6275 Remote Similarity NPC24122
0.6182 Remote Similarity NPC32356
0.6168 Remote Similarity NPC190955
0.598 Remote Similarity NPC120203
0.5949 Remote Similarity NPC469807
0.5865 Remote Similarity NPC11466
0.575 Remote Similarity NPC475082
0.5733 Remote Similarity NPC108375
0.5698 Remote Similarity NPC239931
0.5698 Remote Similarity NPC78954
0.5698 Remote Similarity NPC82770
0.5682 Remote Similarity NPC208302
0.5641 Remote Similarity NPC476214
0.5614 Remote Similarity NPC221877

  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 NPC299367 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
0.625 Remote Similarity NPD745 Clinical (unspecified phase)
0.619 Remote Similarity NPD183 Approved
0.6168 Remote Similarity NPD5278 Discontinued
0.5982 Remote Similarity NPD1944 Phase 2
0.5946 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5893 Remote Similarity NPD1246 Approved
0.5882 Remote Similarity NPD1672 Phase 2
0.5784 Remote Similarity NPD532 Approved
0.5776 Remote Similarity NPD446 Clinical (unspecified phase)
0.5755 Remote Similarity NPD744 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1279 Clinical (unspecified phase)
0.5652 Remote Similarity NPD3907 Clinical (unspecified phase)
0.5641 Remote Similarity NPD1245 Approved
0.5603 Remote Similarity NPD9356 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