Structure

Physi-Chem Properties

Molecular Weight:  277.99
Volume:  256.233
LogP:  4.789
LogD:  3.091
LogS:  -6.165
# Rotatable Bonds:  3
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.736
Synthetic Accessibility Score:  2.476
Fsp3:  0.077
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:  -4.236
MDCK Permeability:  1.234707724506734e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  100.66532897949219%
Volume Distribution (VD):  1.76
Pgp-substrate:  1.5445653200149536%

ADMET: Metabolism

CYP1A2-inhibitor:  0.994
CYP1A2-substrate:  0.407
CYP2C19-inhibitor:  0.953
CYP2C19-substrate:  0.103
CYP2C9-inhibitor:  0.8
CYP2C9-substrate:  0.67
CYP2D6-inhibitor:  0.932
CYP2D6-substrate:  0.896
CYP3A4-inhibitor:  0.942
CYP3A4-substrate:  0.656

ADMET: Excretion

Clearance (CL):  1.91
Half-life (T1/2):  0.008

ADMET: Toxicity

hERG Blockers:  0.032
Human Hepatotoxicity (H-HT):  0.764
Drug-inuced Liver Injury (DILI):  0.913
AMES Toxicity:  0.136
Rat Oral Acute Toxicity:  0.22
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.185
Carcinogencity:  0.175
Eye Corrosion:  0.004
Eye Irritation:  0.718
Respiratory Toxicity:  0.551

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

  Natural Product: NPC173019

Natural Product ID:  NPC173019
Common Name*:   Alpha-Terthienylmethanol
IUPAC Name:   [5-(5-thiophen-2-ylthiophen-2-yl)thiophen-2-yl]methanol
Synonyms:  
Standard InCHIKey:  WAYZWWNNJZMQCQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H10OS3/c14-8-9-3-4-12(16-9)13-6-5-11(17-13)10-2-1-7-15-10/h1-7,14H,8H2
SMILES:  OCc1ccc(s1)c1ccc(s1)c1cccs1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL90170
PubChem CID:   454740
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
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[12608846]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[17880175]
NPO33375 eclipata prostrata Species n.a. n.a. aerial parts n.a. n.a. PMID[25443644]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19837 Euonymus latifolius Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19410 Clutia abyssinica Species Peraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20431 Centaurea canariensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20101 Eria acutifolia Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17908 Rhododendron reticulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17115 Kielmeyera petiolaris Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26309 Ahnfeltiopsis flabelliformis Species Phyllophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19559 Cetraria pseudocomplicata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14172 Rhopaloeides odorabile Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18749 Corydalis vernyi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20233 Marchantia paleacea Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11034 Mnium pseudopunctatum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20982 Morus lactea Species Sulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21251 Tabernaemontana odoratissima Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3468 Astragalus floccosifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19272 Alcyonium fauri Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20648 Streptomyces cellulosae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20718 Hypericum elegans Species Hypericaceae 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
NPT1592 Individual Protein Dipeptidyl peptidase IV Homo sapiens IC50 = 3350.0 nM PMID[521544]
NPT2 Others Unspecified IC50 = 4000.0 nM PMID[521543]

☑ 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 NPC173019 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
0.899 High Similarity NPC472171
0.89 High Similarity NPC472172
0.8627 High Similarity NPC472170
0.8061 Intermediate Similarity NPC2751
0.7872 Intermediate Similarity NPC195713
0.7864 Intermediate Similarity NPC474934
0.7857 Intermediate Similarity NPC221877
0.7407 Intermediate Similarity NPC475115
0.7248 Intermediate Similarity NPC24122
0.7216 Intermediate Similarity NPC8981
0.7094 Intermediate Similarity NPC32356
0.6939 Remote Similarity NPC299367
0.6636 Remote Similarity NPC175376
0.6614 Remote Similarity NPC475082
0.6602 Remote Similarity NPC472169
0.6552 Remote Similarity NPC475086
0.633 Remote Similarity NPC166487
0.625 Remote Similarity NPC117180
0.6224 Remote Similarity NPC105991
0.619 Remote Similarity NPC87299
0.619 Remote Similarity NPC329319
0.619 Remote Similarity NPC99394
0.619 Remote Similarity NPC103326
0.6176 Remote Similarity NPC66655
0.6161 Remote Similarity NPC300455
0.6132 Remote Similarity NPC172984
0.6075 Remote Similarity NPC304538
0.6034 Remote Similarity NPC275104
0.5981 Remote Similarity NPC471895
0.5963 Remote Similarity NPC93843
0.5963 Remote Similarity NPC148231
0.5946 Remote Similarity NPC199567
0.5917 Remote Similarity NPC472919
0.5882 Remote Similarity NPC108218
0.5854 Remote Similarity NPC190955
0.5841 Remote Similarity NPC79917
0.5833 Remote Similarity NPC307163
0.5804 Remote Similarity NPC1793
0.5794 Remote Similarity NPC133050
0.5789 Remote Similarity NPC128645
0.578 Remote Similarity NPC470794
0.5776 Remote Similarity NPC21959
0.5766 Remote Similarity NPC211237
0.5741 Remote Similarity NPC475199
0.5741 Remote Similarity NPC283012
0.5702 Remote Similarity NPC300017
0.5686 Remote Similarity NPC208302
0.5686 Remote Similarity NPC470796
0.566 Remote Similarity NPC224544
0.5648 Remote Similarity NPC471376
0.5636 Remote Similarity NPC168855
0.5612 Remote Similarity NPC22627
0.5606 Remote Similarity NPC112823
0.5603 Remote Similarity NPC325292
0.5603 Remote Similarity NPC138117

  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 NPC173019 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
0.7373 Intermediate Similarity NPD446 Clinical (unspecified phase)
0.6587 Remote Similarity NPD1877 Discontinued
0.6446 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6418 Remote Similarity NPD2202 Clinical (unspecified phase)
0.6387 Remote Similarity NPD5278 Discontinued
0.6269 Remote Similarity NPD4404 Approved
0.623 Remote Similarity NPD1279 Clinical (unspecified phase)
0.6176 Remote Similarity NPD9294 Approved
0.6142 Remote Similarity NPD1245 Approved
0.614 Remote Similarity NPD1672 Phase 2
0.6129 Remote Similarity NPD1246 Approved
0.6115 Remote Similarity NPD7137 Phase 2
0.6087 Remote Similarity NPD5886 Approved
0.6087 Remote Similarity NPD41 Approved
0.6026 Remote Similarity NPD3492 Approved
0.6026 Remote Similarity NPD3493 Approved
0.6026 Remote Similarity NPD3494 Approved
0.597 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5968 Remote Similarity NPD1105 Clinical (unspecified phase)
0.5968 Remote Similarity NPD5277 Phase 2
0.5954 Remote Similarity NPD4273 Approved
0.5833 Remote Similarity NPD5702 Clinical (unspecified phase)
0.5821 Remote Similarity NPD4099 Approved
0.5821 Remote Similarity NPD4100 Approved
0.5785 Remote Similarity NPD745 Clinical (unspecified phase)
0.5781 Remote Similarity NPD3907 Clinical (unspecified phase)
0.5764 Remote Similarity NPD3599 Approved
0.5764 Remote Similarity NPD4127 Clinical (unspecified phase)
0.5692 Remote Similarity NPD7330 Discontinued
0.5664 Remote Similarity NPD2862 Discontinued
0.5641 Remote Similarity NPD5206 Clinical (unspecified phase)
0.5629 Remote Similarity NPD6813 Clinical (unspecified phase)
0.562 Remote Similarity NPD744 Clinical (unspecified phase)
0.5615 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