Structure

Physi-Chem Properties

Molecular Weight:  127.01
Volume:  116.867
LogP:  1.579
LogD:  1.153
LogS:  -1.684
# Rotatable Bonds:  1
TPSA:  32.59
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.346
Synthetic Accessibility Score:  2.648
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:  -4.295
MDCK Permeability:  2.9494487534975633e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.056
20% Bioavailability (F20%):  0.847
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.785
Plasma Protein Binding (PPB):  76.02891540527344%
Volume Distribution (VD):  0.918
Pgp-substrate:  30.373144149780273%

ADMET: Metabolism

CYP1A2-inhibitor:  0.963
CYP1A2-substrate:  0.488
CYP2C19-inhibitor:  0.458
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.046
CYP2C9-substrate:  0.616
CYP2D6-inhibitor:  0.485
CYP2D6-substrate:  0.79
CYP3A4-inhibitor:  0.579
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  1.727
Half-life (T1/2):  0.518

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.111
Drug-inuced Liver Injury (DILI):  0.211
AMES Toxicity:  0.915
Rat Oral Acute Toxicity:  0.629
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.246
Carcinogencity:  0.608
Eye Corrosion:  0.974
Eye Irritation:  0.99
Respiratory Toxicity:  0.937

Download Data

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

  Natural Product: NPC471376

Natural Product ID:  NPC471376
Common Name*:   2-Thiophenecarboxaldehyde Oxime
IUPAC Name:   (NE)-N-(thiophen-2-ylmethylidene)hydroxylamine
Synonyms:  
Standard InCHIKey:  GASLBPLHYRZLLT-GQCTYLIASA-N
Standard InCHI:  InChI=1S/C5H5NOS/c7-6-4-5-2-1-3-8-5/h1-4,7H/b6-4+
SMILES:  O/N=C/c1cccs1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2420347
PubChem CID:   6876527
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004144] Heteroaromatic compounds

*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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens Activity = 93.0 % PMID[475849]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Activity = 58.6 % PMID[475849]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Activity = 8.02 % PMID[475849]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Inhibition = 61.0 % PMID[475849]
NPT65 Cell Line HepG2 Homo sapiens CC50 = 562190.0 nM PMID[475850]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita EC50 > 250.0 ug.mL-1 PMID[475848]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 431230.0 nM PMID[475850]
NPT2 Others Unspecified Ratio CC50/IC50 = 1.59 n.a. PMID[475850]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 353560.0 nM PMID[475850]
NPT2 Others Unspecified Ratio CC50/IC50 = 1.3 n.a. PMID[475850]

☑ 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 NPC471376 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
0.7667 Intermediate Similarity NPC166487
0.7625 Intermediate Similarity NPC470796
0.7419 Intermediate Similarity NPC300455
0.7284 Intermediate Similarity NPC105991
0.7073 Intermediate Similarity NPC470795
0.6629 Remote Similarity NPC8981
0.6556 Remote Similarity NPC195713
0.6522 Remote Similarity NPC471895
0.6522 Remote Similarity NPC307163
0.6517 Remote Similarity NPC299367
0.6449 Remote Similarity NPC190955
0.6436 Remote Similarity NPC120203
0.6395 Remote Similarity NPC125144
0.6395 Remote Similarity NPC121708
0.6311 Remote Similarity NPC11466
0.617 Remote Similarity NPC472169
0.6133 Remote Similarity NPC108375
0.6105 Remote Similarity NPC470794
0.6061 Remote Similarity NPC470797
0.596 Remote Similarity NPC2751
0.5952 Remote Similarity NPC22627
0.5823 Remote Similarity NPC476214
0.5816 Remote Similarity NPC148231
0.5769 Remote Similarity NPC175376
0.5648 Remote Similarity NPC173019

  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 NPC471376 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
0.6907 Remote Similarity NPD532 Approved
0.6699 Remote Similarity NPD745 Clinical (unspecified phase)
0.6635 Remote Similarity NPD183 Approved
0.6505 Remote Similarity NPD793 Approved
0.6337 Remote Similarity NPD1672 Phase 2
0.6262 Remote Similarity NPD445 Discontinued
0.6053 Remote Similarity NPD3907 Clinical (unspecified phase)
0.6019 Remote Similarity NPD9702 Discontinued
0.6 Remote Similarity NPD9356 Discontinued
0.5966 Remote Similarity NPD5702 Clinical (unspecified phase)
0.5872 Remote Similarity NPD3459 Approved
0.5826 Remote Similarity NPD1944 Phase 2
0.5766 Remote Similarity NPD2242 Phase 1
0.5678 Remote Similarity NPD483 Approved

  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