Structure

Physi-Chem Properties

Molecular Weight:  280.02
Volume:  263.861
LogP:  2.502
LogD:  2.844
LogS:  -3.379
# Rotatable Bonds:  3
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.75
Synthetic Accessibility Score:  3.545
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:  -4.717
MDCK Permeability:  0.00014602502051275223
Pgp-inhibitor:  0.003
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.505
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  99.31132507324219%
Volume Distribution (VD):  0.99
Pgp-substrate:  1.6608330011367798%

ADMET: Metabolism

CYP1A2-inhibitor:  0.904
CYP1A2-substrate:  0.091
CYP2C19-inhibitor:  0.839
CYP2C19-substrate:  0.226
CYP2C9-inhibitor:  0.878
CYP2C9-substrate:  0.713
CYP2D6-inhibitor:  0.143
CYP2D6-substrate:  0.372
CYP3A4-inhibitor:  0.508
CYP3A4-substrate:  0.462

ADMET: Excretion

Clearance (CL):  2.685
Half-life (T1/2):  0.061

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.788
Drug-inuced Liver Injury (DILI):  0.977
AMES Toxicity:  0.282
Rat Oral Acute Toxicity:  0.421
Maximum Recommended Daily Dose:  0.824
Skin Sensitization:  0.694
Carcinogencity:  0.892
Eye Corrosion:  0.004
Eye Irritation:  0.406
Respiratory Toxicity:  0.922

Download Data

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

  Natural Product: NPC472170

Natural Product ID:  NPC472170
Common Name*:   4-(5'-(Hydroxymethyl)-2,2'-Bithiophen-5-Yl)But-3-Yne-1,2-Diol
IUPAC Name:   4-[5-[5-(hydroxymethyl)thiophen-2-yl]thiophen-2-yl]but-3-yne-1,2-diol
Synonyms:  
Standard InCHIKey:  WNRIEIDIQRVQRK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H12O3S2/c14-7-9(16)1-2-10-3-5-12(17-10)13-6-4-11(8-15)18-13/h3-6,9,14-16H,7-8H2
SMILES:  OCc1ccc(s1)c1ccc(s1)C#CC(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3343900
PubChem CID:   46842529
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
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 = 2810.0 nM PMID[523419]

☑ 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 NPC472170 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
0.9175 High Similarity NPC474934
0.8627 High Similarity NPC173019
0.8454 Intermediate Similarity NPC2751
0.8095 Intermediate Similarity NPC475115
0.7835 Intermediate Similarity NPC472169
0.7757 Intermediate Similarity NPC472171
0.7685 Intermediate Similarity NPC472172
0.7565 Intermediate Similarity NPC32356
0.7477 Intermediate Similarity NPC475086
0.732 Intermediate Similarity NPC299367
0.7245 Intermediate Similarity NPC8981
0.7177 Intermediate Similarity NPC475082
0.6975 Remote Similarity NPC221877
0.6667 Remote Similarity NPC195713
0.6442 Remote Similarity NPC117180
0.6381 Remote Similarity NPC99394
0.6381 Remote Similarity NPC87299
0.6381 Remote Similarity NPC329319
0.6381 Remote Similarity NPC103326
0.6372 Remote Similarity NPC175376
0.6263 Remote Similarity NPC105991
0.6262 Remote Similarity NPC304538
0.6239 Remote Similarity NPC24122
0.6218 Remote Similarity NPC472919
0.6058 Remote Similarity NPC66655
0.6019 Remote Similarity NPC172984
0.5983 Remote Similarity NPC210529
0.5983 Remote Similarity NPC160548
0.5983 Remote Similarity NPC175852
0.5982 Remote Similarity NPC1793
0.5948 Remote Similarity NPC21959
0.5946 Remote Similarity NPC211237
0.5932 Remote Similarity NPC275104
0.5929 Remote Similarity NPC166487
0.5926 Remote Similarity NPC475199
0.5926 Remote Similarity NPC283012
0.5917 Remote Similarity NPC82426
0.5917 Remote Similarity NPC91820
0.5913 Remote Similarity NPC325292
0.5913 Remote Similarity NPC138117
0.5909 Remote Similarity NPC99482
0.5877 Remote Similarity NPC300017
0.5856 Remote Similarity NPC93843
0.5841 Remote Similarity NPC199567
0.5833 Remote Similarity NPC60373
0.5833 Remote Similarity NPC133050
0.5833 Remote Similarity NPC154905
0.5818 Remote Similarity NPC470794
0.5812 Remote Similarity NPC313650
0.5798 Remote Similarity NPC78119
0.5798 Remote Similarity NPC51333
0.5798 Remote Similarity NPC216468
0.5798 Remote Similarity NPC132078
0.5785 Remote Similarity NPC160382
0.5776 Remote Similarity NPC300455
0.5769 Remote Similarity NPC108218
0.575 Remote Similarity NPC294741
0.575 Remote Similarity NPC213730
0.5739 Remote Similarity NPC79917
0.5738 Remote Similarity NPC148060
0.5738 Remote Similarity NPC171831
0.5738 Remote Similarity NPC242913
0.5738 Remote Similarity NPC315794
0.5738 Remote Similarity NPC280616
0.5736 Remote Similarity NPC210531
0.5726 Remote Similarity NPC20142
0.5726 Remote Similarity NPC277788
0.5726 Remote Similarity NPC215351
0.5714 Remote Similarity NPC148231
0.5714 Remote Similarity NPC474073
0.5714 Remote Similarity NPC474211
0.5702 Remote Similarity NPC40258
0.5702 Remote Similarity NPC7686
0.5702 Remote Similarity NPC110764
0.5702 Remote Similarity NPC104216
0.5702 Remote Similarity NPC91461
0.569 Remote Similarity NPC128645
0.5676 Remote Similarity NPC168855
0.5669 Remote Similarity NPC185840
0.5645 Remote Similarity NPC37115
0.5645 Remote Similarity NPC136962
0.5636 Remote Similarity NPC73637
0.5636 Remote Similarity NPC121478
0.5635 Remote Similarity NPC55617
0.5635 Remote Similarity NPC62258
0.5635 Remote Similarity NPC190955
0.563 Remote Similarity NPC289201
0.5625 Remote Similarity NPC474354
0.562 Remote Similarity NPC469481
0.561 Remote Similarity NPC249067
0.561 Remote Similarity NPC12278
0.5603 Remote Similarity NPC47950
0.5603 Remote Similarity NPC317645
0.5603 Remote Similarity NPC312304
0.5603 Remote Similarity NPC277758
0.5603 Remote Similarity NPC300478
0.56 Remote Similarity NPC251306

  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 NPC472170 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
0.7542 Intermediate Similarity NPD446 Clinical (unspecified phase)
0.6692 Remote Similarity NPD2202 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4404 Approved
0.6484 Remote Similarity NPD1877 Discontinued
0.6471 Remote Similarity NPD41 Approved
0.6471 Remote Similarity NPD5886 Approved
0.6377 Remote Similarity NPD7137 Phase 2
0.629 Remote Similarity NPD1246 Approved
0.621 Remote Similarity NPD1280 Clinical (unspecified phase)
0.6148 Remote Similarity NPD5278 Discontinued
0.6058 Remote Similarity NPD9294 Approved
0.6053 Remote Similarity NPD3494 Approved
0.6053 Remote Similarity NPD3493 Approved
0.6053 Remote Similarity NPD3492 Approved
0.6047 Remote Similarity NPD1245 Approved
0.6 Remote Similarity NPD2158 Clinical (unspecified phase)
0.6 Remote Similarity NPD1279 Clinical (unspecified phase)
0.5983 Remote Similarity NPD9495 Approved
0.5917 Remote Similarity NPD744 Clinical (unspecified phase)
0.5865 Remote Similarity NPD4273 Approved
0.5763 Remote Similarity NPD1672 Phase 2
0.5748 Remote Similarity NPD1105 Clinical (unspecified phase)
0.5748 Remote Similarity NPD5277 Phase 2
0.5725 Remote Similarity NPD7330 Discontinued
0.5704 Remote Similarity NPD7876 Discontinued
0.5692 Remote Similarity NPD7636 Approved
0.5658 Remote Similarity NPD6813 Clinical (unspecified phase)
0.5652 Remote Similarity NPD767 Phase 1
0.563 Remote Similarity NPD5702 Clinical (unspecified phase)
0.562 Remote Similarity NPD4100 Approved
0.562 Remote Similarity NPD4099 Approved
0.561 Remote Similarity NPD1237 Approved
0.5603 Remote Similarity NPD4248 Discontinued
0.56 Remote Similarity NPD9532 Phase 3

  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