Structure

Physi-Chem Properties

Molecular Weight:  381.18
Volume:  379.413
LogP:  0.464
LogD:  0.48
LogS:  -0.853
# Rotatable Bonds:  1
TPSA:  113.37
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.481
Synthetic Accessibility Score:  5.64
Fsp3:  0.632
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:  -4.861
MDCK Permeability:  4.5292010327102616e-05
Pgp-inhibitor:  0.063
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.974
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.451
Plasma Protein Binding (PPB):  25.008089065551758%
Volume Distribution (VD):  1.102
Pgp-substrate:  66.880126953125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.673
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.107
CYP2D6-inhibitor:  0.044
CYP2D6-substrate:  0.612
CYP3A4-inhibitor:  0.048
CYP3A4-substrate:  0.486

ADMET: Excretion

Clearance (CL):  3.206
Half-life (T1/2):  0.495

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.273
Drug-inuced Liver Injury (DILI):  0.513
AMES Toxicity:  0.986
Rat Oral Acute Toxicity:  0.143
Maximum Recommended Daily Dose:  0.901
Skin Sensitization:  0.891
Carcinogencity:  0.541
Eye Corrosion:  0.005
Eye Irritation:  0.013
Respiratory Toxicity:  0.042

Download Data

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

  Natural Product: NPC2751

Natural Product ID:  NPC2751
Common Name*:   [5-[(E)-Hept-5-En-1,3-Diynyl]Thiophen-2-Yl]Methanol
IUPAC Name:   [5-[(E)-hept-5-en-1,3-diynyl]thiophen-2-yl]methanol
Synonyms:  
Standard InCHIKey:  XFCGMIGOOIZCKE-NSCUHMNNSA-N
Standard InCHI:  InChI=1S/C12H10OS/c1-2-3-4-5-6-7-11-8-9-12(10-13)14-11/h2-3,8-9,13H,10H2,1H3/b3-2+
SMILES:  C/C=C/C#CC#Cc1ccc(CO)s1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL500347
PubChem CID:   44583855
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
NPO24814 Xanthopappus subacaulis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16933888]
NPO24814 Xanthopappus subacaulis Species 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
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 = 0.3 ug.mL-1 PMID[541386]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 > 10.0 ug.mL-1 PMID[541386]

☑ 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 NPC2751 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
0.9222 High Similarity NPC474934
0.883 High Similarity NPC475115
0.8675 High Similarity NPC299367
0.8454 Intermediate Similarity NPC472170
0.8182 Intermediate Similarity NPC472169
0.8061 Intermediate Similarity NPC173019
0.7573 Intermediate Similarity NPC475086
0.7412 Intermediate Similarity NPC105991
0.7353 Intermediate Similarity NPC472171
0.7282 Intermediate Similarity NPC472172
0.7027 Intermediate Similarity NPC32356
0.6869 Remote Similarity NPC166487
0.6774 Remote Similarity NPC8981
0.6667 Remote Similarity NPC475082
0.6667 Remote Similarity NPC300455
0.6435 Remote Similarity NPC221877
0.6429 Remote Similarity NPC470794
0.6392 Remote Similarity NPC103326
0.6392 Remote Similarity NPC87299
0.6392 Remote Similarity NPC99394
0.6392 Remote Similarity NPC329319
0.6383 Remote Similarity NPC66655
0.6327 Remote Similarity NPC172984
0.6327 Remote Similarity NPC307163
0.6327 Remote Similarity NPC471895
0.6289 Remote Similarity NPC117180
0.6283 Remote Similarity NPC190955
0.6263 Remote Similarity NPC304538
0.6186 Remote Similarity NPC195713
0.6139 Remote Similarity NPC93843
0.6087 Remote Similarity NPC470795
0.6022 Remote Similarity NPC470796
0.6 Remote Similarity NPC79917
0.5962 Remote Similarity NPC1793
0.596 Remote Similarity NPC133050
0.596 Remote Similarity NPC471376
0.5955 Remote Similarity NPC22627
0.5926 Remote Similarity NPC175376
0.5909 Remote Similarity NPC275104
0.5905 Remote Similarity NPC470797
0.5895 Remote Similarity NPC100980
0.5895 Remote Similarity NPC108218
0.5849 Remote Similarity NPC277758
0.5825 Remote Similarity NPC148231
0.5816 Remote Similarity NPC224544
0.581 Remote Similarity NPC199567
0.581 Remote Similarity NPC104216
0.5804 Remote Similarity NPC24122
0.5789 Remote Similarity NPC472919
0.5784 Remote Similarity NPC168855
0.5769 Remote Similarity NPC211237
0.5741 Remote Similarity NPC138117
0.5741 Remote Similarity NPC325292
0.5728 Remote Similarity NPC474354
0.5701 Remote Similarity NPC300017
0.5699 Remote Similarity NPC239931
0.5699 Remote Similarity NPC78954
0.5699 Remote Similarity NPC82770
0.5684 Remote Similarity NPC208302
0.5673 Remote Similarity NPC474211
0.5673 Remote Similarity NPC248817
0.5657 Remote Similarity NPC65517
0.5648 Remote Similarity NPC314690
0.5648 Remote Similarity NPC265521
0.5648 Remote Similarity NPC128645
0.5636 Remote Similarity NPC313650
0.5636 Remote Similarity NPC21959
0.5619 Remote Similarity NPC198747
0.5619 Remote Similarity NPC197783
0.56 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 NPC2751 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
0.6724 Remote Similarity NPD446 Clinical (unspecified phase)
0.6383 Remote Similarity NPD9294 Approved
0.6364 Remote Similarity NPD1877 Discontinued
0.6261 Remote Similarity NPD1105 Clinical (unspecified phase)
0.6207 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6202 Remote Similarity NPD2202 Clinical (unspecified phase)
0.6154 Remote Similarity NPD1246 Approved
0.614 Remote Similarity NPD5278 Discontinued
0.6047 Remote Similarity NPD4404 Approved
0.5985 Remote Similarity NPD5886 Approved
0.5985 Remote Similarity NPD41 Approved
0.5983 Remote Similarity NPD1279 Clinical (unspecified phase)
0.5983 Remote Similarity NPD5277 Phase 2
0.5902 Remote Similarity NPD1245 Approved
0.5896 Remote Similarity NPD7137 Phase 2
0.5895 Remote Similarity NPD9087 Approved
0.5868 Remote Similarity NPD9356 Discontinued
0.584 Remote Similarity NPD4273 Approved
0.5789 Remote Similarity NPD745 Clinical (unspecified phase)
0.5739 Remote Similarity NPD183 Approved
0.5657 Remote Similarity NPD9088 Approved
0.5656 Remote Similarity NPD3907 Clinical (unspecified phase)
0.5644 Remote Similarity NPD9250 Approved
0.5615 Remote Similarity NPD2035 Discontinued
0.5615 Remote Similarity NPD2158 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