Structure

Physi-Chem Properties

Molecular Weight:  133.99
Volume:  128.46
LogP:  1.49
LogD:  1.176
LogS:  -3.223
# Rotatable Bonds:  0
TPSA:  47.58
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.539
Synthetic Accessibility Score:  3.007
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.201
MDCK Permeability:  1.9033059288631193e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.277

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.08
Plasma Protein Binding (PPB):  83.39395904541016%
Volume Distribution (VD):  1.179
Pgp-substrate:  6.756287097930908%

ADMET: Metabolism

CYP1A2-inhibitor:  0.974
CYP1A2-substrate:  0.345
CYP2C19-inhibitor:  0.6
CYP2C19-substrate:  0.102
CYP2C9-inhibitor:  0.326
CYP2C9-substrate:  0.471
CYP2D6-inhibitor:  0.052
CYP2D6-substrate:  0.602
CYP3A4-inhibitor:  0.106
CYP3A4-substrate:  0.393

ADMET: Excretion

Clearance (CL):  7.157
Half-life (T1/2):  0.509

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.975
Drug-inuced Liver Injury (DILI):  0.905
AMES Toxicity:  0.33
Rat Oral Acute Toxicity:  0.402
Maximum Recommended Daily Dose:  0.359
Skin Sensitization:  0.273
Carcinogencity:  0.924
Eye Corrosion:  0.985
Eye Irritation:  0.994
Respiratory Toxicity:  0.955

Download Data

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

  Natural Product: NPC470795

Natural Product ID:  NPC470795
Common Name*:   2,5-Thiophenedinitrile
IUPAC Name:   thiophene-2,5-dicarbonitrile
Synonyms:  
Standard InCHIKey:  MYINLNBRJVGINA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H2N2S/c7-3-5-1-2-6(4-8)9-5/h1-2H
SMILES:  C1=C(SC(=C1)C#N)C#N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229529
PubChem CID:   140436
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
NPO1099 Capparis spinosa Species Capparaceae Eukaryota aerial parts and buds Cagliari, Sardinia 2012-FEB PMID[22769561]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

☑ 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
NPT450 Organism Meloidogyne incognita Meloidogyne incognita EC50 > 250.0 ug.mL-1 PMID[452837]

☑ 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 NPC470795 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
0.9265 High Similarity NPC470796
0.7529 Intermediate Similarity NPC470797
0.7333 Intermediate Similarity NPC105991
0.7073 Intermediate Similarity NPC471376
0.6914 Remote Similarity NPC299367
0.6829 Remote Similarity NPC8981
0.6747 Remote Similarity NPC195713
0.6533 Remote Similarity NPC22627
0.6512 Remote Similarity NPC307163
0.6512 Remote Similarity NPC472169
0.6437 Remote Similarity NPC470794
0.6374 Remote Similarity NPC166487
0.6322 Remote Similarity NPC471895
0.6292 Remote Similarity NPC148231
0.617 Remote Similarity NPC300455
0.6087 Remote Similarity NPC108375
0.6087 Remote Similarity NPC2751
0.5918 Remote Similarity NPC120203
0.5875 Remote Similarity NPC52330
0.5867 Remote Similarity NPC469807
0.58 Remote Similarity NPC11466
0.5753 Remote Similarity NPC476214
0.5714 Remote Similarity NPC175376
0.5696 Remote Similarity NPC50266
0.5657 Remote Similarity NPC474934

  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 NPC470795 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
0.6211 Remote Similarity NPD532 Approved
0.6146 Remote Similarity NPD1672 Phase 2
0.5842 Remote Similarity NPD793 Approved
0.5825 Remote Similarity NPD9702 Discontinued
0.5769 Remote Similarity NPD445 Discontinued
0.5673 Remote Similarity NPD3459 Approved
0.5625 Remote Similarity NPD173 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