Structure

Physi-Chem Properties

Molecular Weight:  211.05
Volume:  197.429
LogP:  -0.641
LogD:  -0.396
LogS:  -0.913
# Rotatable Bonds:  4
TPSA:  107.72
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.458
Synthetic Accessibility Score:  3.014
Fsp3:  0.222
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.781
MDCK Permeability:  0.0003027740749530494
Pgp-inhibitor:  0.0
Pgp-substrate:  0.522
Human Intestinal Absorption (HIA):  0.033
20% Bioavailability (F20%):  0.032
30% Bioavailability (F30%):  0.944

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.35
Plasma Protein Binding (PPB):  49.48139953613281%
Volume Distribution (VD):  0.585
Pgp-substrate:  69.0307846069336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.064
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.043
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.084
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.118
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  1.908
Half-life (T1/2):  0.873

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.231
Drug-inuced Liver Injury (DILI):  0.96
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.102
Skin Sensitization:  0.65
Carcinogencity:  0.013
Eye Corrosion:  0.003
Eye Irritation:  0.585
Respiratory Toxicity:  0.933

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

  Natural Product: NPC202056

Natural Product ID:  NPC202056
Common Name*:   (S)-4-(2-Oxoethylidene)-1,2,3,4-Tetrahydropyridine-2,6-Dicarboxylic Acid
IUPAC Name:   (2S,4E)-4-(2-oxoethylidene)-2,3-dihydro-1H-pyridine-2,6-dicarboxylic acid
Synonyms:  
Standard InCHIKey:  YQDKULBMDMPFLH-FSRBREEPSA-N
Standard InCHI:  InChI=1S/C9H9NO5/c11-2-1-5-3-6(8(12)13)10-7(4-5)9(14)15/h1-3,7,10H,4H2,(H,12,13)(H,14,15)/b5-1-/t7-/m0/s1
SMILES:  O=C/C=C/1C[C@H](NC(=C1)C(=O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2062984
PubChem CID:   5281176
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[33118348]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO27911 Celosia cristata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27911 Celosia cristata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27911 Celosia cristata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7507 Portulaca grandiflora Species Portulacaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 2.7 equiv PMID[503909]

☑ 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 NPC202056 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
0.7216 Intermediate Similarity NPC313265
0.7108 Intermediate Similarity NPC7392
0.7108 Intermediate Similarity NPC98329
0.7059 Intermediate Similarity NPC133700
0.6747 Remote Similarity NPC4668
0.6747 Remote Similarity NPC133758
0.64 Remote Similarity NPC236322
0.6395 Remote Similarity NPC314221
0.6395 Remote Similarity NPC60424
0.6353 Remote Similarity NPC50047
0.6154 Remote Similarity NPC40663
0.6132 Remote Similarity NPC473364
0.6092 Remote Similarity NPC112312
0.6022 Remote Similarity NPC122471
0.6 Remote Similarity NPC305973
0.5929 Remote Similarity NPC298484
0.59 Remote Similarity NPC296589
0.5895 Remote Similarity NPC314680
0.5851 Remote Similarity NPC281154
0.5806 Remote Similarity NPC475610
0.5804 Remote Similarity NPC185929
0.5804 Remote Similarity NPC471259
0.58 Remote Similarity NPC475975
0.5795 Remote Similarity NPC66789
0.5743 Remote Similarity NPC90476
0.5743 Remote Similarity NPC69374
0.5728 Remote Similarity NPC320057
0.569 Remote Similarity NPC59249
0.5686 Remote Similarity NPC469861
0.5686 Remote Similarity NPC476141
0.5686 Remote Similarity NPC130436
0.5686 Remote Similarity NPC469860
0.568 Remote Similarity NPC473249
0.5657 Remote Similarity NPC226982
0.5657 Remote Similarity NPC277341
0.5648 Remote Similarity NPC471257
0.5638 Remote Similarity NPC26932
0.5612 Remote Similarity NPC157173

  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 NPC202056 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
0.7108 Intermediate Similarity NPD9137 Approved
0.5917 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5913 Remote Similarity NPD2090 Approved
0.5868 Remote Similarity NPD7623 Phase 3
0.5868 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9109 Discontinued
0.5798 Remote Similarity NPD2099 Approved
0.5766 Remote Similarity NPD2905 Discontinued
0.5684 Remote Similarity NPD1452 Discontinued
0.568 Remote Similarity NPD7747 Phase 1
0.568 Remote Similarity NPD7746 Phase 1
0.566 Remote Similarity NPD2251 Approved
0.566 Remote Similarity NPD2252 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