Structure

Physi-Chem Properties

Molecular Weight:  136.99
Volume:  128.89
LogP:  1.158
LogD:  1.119
LogS:  -2.245
# Rotatable Bonds:  1
TPSA:  40.86
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.549
Synthetic Accessibility Score:  2.971
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.306
MDCK Permeability:  1.7158239643322304e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.343
30% Bioavailability (F30%):  0.539

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.063
Plasma Protein Binding (PPB):  83.22554779052734%
Volume Distribution (VD):  0.682
Pgp-substrate:  9.937170028686523%

ADMET: Metabolism

CYP1A2-inhibitor:  0.967
CYP1A2-substrate:  0.135
CYP2C19-inhibitor:  0.531
CYP2C19-substrate:  0.096
CYP2C9-inhibitor:  0.173
CYP2C9-substrate:  0.685
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.513
CYP3A4-inhibitor:  0.027
CYP3A4-substrate:  0.274

ADMET: Excretion

Clearance (CL):  6.737
Half-life (T1/2):  0.457

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.765
Drug-inuced Liver Injury (DILI):  0.534
AMES Toxicity:  0.754
Rat Oral Acute Toxicity:  0.127
Maximum Recommended Daily Dose:  0.106
Skin Sensitization:  0.403
Carcinogencity:  0.819
Eye Corrosion:  0.957
Eye Irritation:  0.995
Respiratory Toxicity:  0.933

Download Data

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

  Natural Product: NPC470797

Natural Product ID:  NPC470797
Common Name*:   5-Formylthiophene-2-Carbonitrile
IUPAC Name:   5-formylthiophene-2-carbonitrile
Synonyms:  
Standard InCHIKey:  PZIFYWVUYHMYOA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H3NOS/c7-3-5-1-2-6(4-8)9-5/h1-2,4H
SMILES:  C1=C(SC(=C1)C#N)C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229532
PubChem CID:   12280004
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[456511]

☑ 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 NPC470797 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
0.8837 High Similarity NPC470794
0.8506 High Similarity NPC471895
0.7889 Intermediate Similarity NPC307163
0.7529 Intermediate Similarity NPC470795
0.7451 Intermediate Similarity NPC24122
0.7442 Intermediate Similarity NPC470796
0.7129 Intermediate Similarity NPC175376
0.6593 Remote Similarity NPC327330
0.6421 Remote Similarity NPC299367
0.6204 Remote Similarity NPC120203
0.61 Remote Similarity NPC472169
0.6091 Remote Similarity NPC11466
0.6061 Remote Similarity NPC471376
0.6042 Remote Similarity NPC78500
0.6022 Remote Similarity NPC105991
0.5905 Remote Similarity NPC2751
0.5849 Remote Similarity NPC166487
0.5812 Remote Similarity NPC190955
0.5743 Remote Similarity NPC100039
0.5743 Remote Similarity NPC73978
0.57 Remote Similarity NPC8981
0.5688 Remote Similarity NPC300455
0.5644 Remote Similarity NPC195713
0.5639 Remote Similarity NPC130655
0.5631 Remote Similarity NPC197581
0.5631 Remote Similarity NPC39600

  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 NPC470797 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
0.6759 Remote Similarity NPD745 Clinical (unspecified phase)
0.6697 Remote Similarity NPD183 Approved
0.6102 Remote Similarity NPD1246 Approved
0.592 Remote Similarity NPD3355 Approved
0.592 Remote Similarity NPD3356 Approved
0.5854 Remote Similarity NPD1245 Approved
0.5667 Remote Similarity NPD1279 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