Structure

Physi-Chem Properties

Molecular Weight:  232.06
Volume:  242.482
LogP:  2.741
LogD:  1.689
LogS:  -3.108
# Rotatable Bonds:  2
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.762
Synthetic Accessibility Score:  4.163
Fsp3:  0.231
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:  -3.97
MDCK Permeability:  3.145610753563233e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.565
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.813

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  100.0662612915039%
Volume Distribution (VD):  1.146
Pgp-substrate:  1.6650269031524658%

ADMET: Metabolism

CYP1A2-inhibitor:  0.928
CYP1A2-substrate:  0.476
CYP2C19-inhibitor:  0.954
CYP2C19-substrate:  0.64
CYP2C9-inhibitor:  0.937
CYP2C9-substrate:  0.972
CYP2D6-inhibitor:  0.774
CYP2D6-substrate:  0.846
CYP3A4-inhibitor:  0.77
CYP3A4-substrate:  0.43

ADMET: Excretion

Clearance (CL):  3.636
Half-life (T1/2):  0.104

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.385
Drug-inuced Liver Injury (DILI):  0.979
AMES Toxicity:  0.816
Rat Oral Acute Toxicity:  0.468
Maximum Recommended Daily Dose:  0.057
Skin Sensitization:  0.884
Carcinogencity:  0.867
Eye Corrosion:  0.036
Eye Irritation:  0.834
Respiratory Toxicity:  0.691

Download Data

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

  Natural Product: NPC474934

Natural Product ID:  NPC474934
Common Name*:   1-[5-[(E)-Hept-5-En-1,3-Diynyl]Thiophen-2-Yl]Ethane-1,2-Diol
IUPAC Name:   1-[5-[(E)-hept-5-en-1,3-diynyl]thiophen-2-yl]ethane-1,2-diol
Synonyms:  
Standard InCHIKey:  RCBXJOCDSLBWEX-NSCUHMNNSA-N
Standard InCHI:  InChI=1S/C13H12O2S/c1-2-3-4-5-6-7-11-8-9-13(16-11)12(15)10-14/h2-3,8-9,12,14-15H,10H2,1H3/b3-2+
SMILES:  CC=CC#CC#CC1=CC=C(S1)C(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL488490
PubChem CID:   10353885
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 = 4.2 ug.mL-1 PMID[538509]
NPT6274 Organism Aedes albopictus Aedes albopictus LC50 > 10.0 ug.mL-1 PMID[538509]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 28200.0 nM PMID[538510]

☑ 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 NPC474934 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 NPC2751
0.9175 High Similarity NPC472170
0.8776 High Similarity NPC475115
0.8556 High Similarity NPC472169
0.8077 Intermediate Similarity NPC475086
0.8 Intermediate Similarity NPC299367
0.7864 Intermediate Similarity NPC173019
0.7196 Intermediate Similarity NPC472171
0.713 Intermediate Similarity NPC472172
0.7043 Intermediate Similarity NPC32356
0.6848 Remote Similarity NPC105991
0.6829 Remote Similarity NPC475082
0.66 Remote Similarity NPC87299
0.66 Remote Similarity NPC329319
0.66 Remote Similarity NPC99394
0.66 Remote Similarity NPC103326
0.65 Remote Similarity NPC117180
0.6471 Remote Similarity NPC304538
0.6471 Remote Similarity NPC221877
0.6465 Remote Similarity NPC8981
0.6415 Remote Similarity NPC166487
0.6404 Remote Similarity NPC472919
0.6263 Remote Similarity NPC66655
0.6239 Remote Similarity NPC300455
0.6214 Remote Similarity NPC172984
0.6168 Remote Similarity NPC1793
0.6154 Remote Similarity NPC470794
0.6091 Remote Similarity NPC138117
0.6091 Remote Similarity NPC325292
0.6058 Remote Similarity NPC307163
0.605 Remote Similarity NPC190955
0.6038 Remote Similarity NPC93843
0.6019 Remote Similarity NPC133050
0.6018 Remote Similarity NPC210529
0.6018 Remote Similarity NPC175852
0.6018 Remote Similarity NPC160548
0.6 Remote Similarity NPC60373
0.6 Remote Similarity NPC154905
0.5982 Remote Similarity NPC313650
0.5981 Remote Similarity NPC211237
0.5965 Remote Similarity NPC275104
0.5948 Remote Similarity NPC91820
0.5948 Remote Similarity NPC82426
0.5948 Remote Similarity NPC160382
0.5922 Remote Similarity NPC195713
0.5909 Remote Similarity NPC79917
0.5909 Remote Similarity NPC300017
0.5905 Remote Similarity NPC471895
0.5897 Remote Similarity NPC148060
0.5897 Remote Similarity NPC315794
0.5888 Remote Similarity NPC474211
0.5877 Remote Similarity NPC474073
0.5872 Remote Similarity NPC104216
0.5862 Remote Similarity NPC471578
0.5862 Remote Similarity NPC101025
0.5849 Remote Similarity NPC168855
0.5841 Remote Similarity NPC175376
0.5841 Remote Similarity NPC21959
0.5825 Remote Similarity NPC469894
0.581 Remote Similarity NPC283012
0.581 Remote Similarity NPC475199
0.58 Remote Similarity NPC108218
0.5798 Remote Similarity NPC136962
0.5794 Remote Similarity NPC474354
0.5794 Remote Similarity NPC99482
0.5776 Remote Similarity NPC469481
0.5769 Remote Similarity NPC328178
0.5766 Remote Similarity NPC47950
0.5766 Remote Similarity NPC300478
0.5766 Remote Similarity NPC277758
0.5766 Remote Similarity NPC312304
0.5763 Remote Similarity NPC280616
0.5763 Remote Similarity NPC242913
0.5763 Remote Similarity NPC171831
0.5752 Remote Similarity NPC215351
0.5752 Remote Similarity NPC20142
0.575 Remote Similarity NPC251306
0.575 Remote Similarity NPC277788
0.5739 Remote Similarity NPC226096
0.5739 Remote Similarity NPC290515
0.5739 Remote Similarity NPC303611
0.5739 Remote Similarity NPC108606
0.5739 Remote Similarity NPC164514
0.5738 Remote Similarity NPC476003
0.5736 Remote Similarity NPC86966
0.5728 Remote Similarity NPC224544
0.5727 Remote Similarity NPC199567
0.5726 Remote Similarity NPC110764
0.5726 Remote Similarity NPC301735
0.5714 Remote Similarity NPC204932
0.5714 Remote Similarity NPC471133
0.5714 Remote Similarity NPC265521
0.569 Remote Similarity NPC78119
0.569 Remote Similarity NPC51333
0.569 Remote Similarity NPC216468
0.569 Remote Similarity NPC131587
0.569 Remote Similarity NPC132078
0.569 Remote Similarity NPC128723
0.5667 Remote Similarity NPC474376
0.5667 Remote Similarity NPC475203
0.5667 Remote Similarity NPC472316
0.5667 Remote Similarity NPC37115
0.5667 Remote Similarity NPC472315
0.566 Remote Similarity NPC106313
0.5659 Remote Similarity NPC112823
0.5657 Remote Similarity NPC470795
0.5656 Remote Similarity NPC473524
0.5645 Remote Similarity NPC115379
0.5644 Remote Similarity NPC100980
0.5641 Remote Similarity NPC214200
0.5641 Remote Similarity NPC289117
0.5641 Remote Similarity NPC294741
0.5641 Remote Similarity NPC228400
0.5641 Remote Similarity NPC328793
0.5641 Remote Similarity NPC213730
0.5641 Remote Similarity NPC174911
0.5636 Remote Similarity NPC407
0.5636 Remote Similarity NPC304760
0.5636 Remote Similarity NPC23167
0.5636 Remote Similarity NPC307235
0.563 Remote Similarity NPC12278
0.5625 Remote Similarity NPC318429
0.5625 Remote Similarity NPC317645
0.562 Remote Similarity NPC194034
0.561 Remote Similarity NPC264784
0.5603 Remote Similarity NPC475954
0.56 Remote Similarity NPC208302
0.56 Remote Similarity NPC470796

  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 NPC474934 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
0.7034 Intermediate Similarity NPD446 Clinical (unspecified phase)
0.6744 Remote Similarity NPD2202 Clinical (unspecified phase)
0.6589 Remote Similarity NPD4404 Approved
0.6532 Remote Similarity NPD1877 Discontinued
0.6515 Remote Similarity NPD41 Approved
0.6515 Remote Similarity NPD5886 Approved
0.6333 Remote Similarity NPD1246 Approved
0.6263 Remote Similarity NPD9294 Approved
0.625 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6186 Remote Similarity NPD5278 Discontinued
0.6176 Remote Similarity NPD7137 Phase 2
0.608 Remote Similarity NPD1245 Approved
0.6033 Remote Similarity NPD1279 Clinical (unspecified phase)
0.6033 Remote Similarity NPD5277 Phase 2
0.6033 Remote Similarity NPD1105 Clinical (unspecified phase)
0.6018 Remote Similarity NPD9495 Approved
0.6016 Remote Similarity NPD4273 Approved
0.5948 Remote Similarity NPD744 Clinical (unspecified phase)
0.5909 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5789 Remote Similarity NPD767 Phase 1
0.5739 Remote Similarity NPD9609 Approved
0.5739 Remote Similarity NPD9611 Approved
0.5739 Remote Similarity NPD9612 Approved
0.5735 Remote Similarity NPD4248 Discontinued
0.5714 Remote Similarity NPD2862 Discontinued
0.5714 Remote Similarity NPD9250 Approved
0.5714 Remote Similarity NPD7636 Approved
0.5658 Remote Similarity NPD3494 Approved
0.5658 Remote Similarity NPD3493 Approved
0.5658 Remote Similarity NPD3492 Approved
0.5644 Remote Similarity NPD9087 Approved
0.5643 Remote Similarity NPD7305 Phase 1
0.5641 Remote Similarity NPD9248 Phase 1
0.5625 Remote Similarity NPD9365 Approved
0.5625 Remote Similarity NPD7330 Discontinued
0.562 Remote Similarity NPD290 Approved
0.562 Remote Similarity NPD9532 Phase 3
0.5606 Remote Similarity NPD7876 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