Structure

Physi-Chem Properties

Molecular Weight:  232.15
Volume:  251.998
LogP:  3.164
LogD:  2.983
LogS:  -3.246
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.364
Synthetic Accessibility Score:  4.34
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.556
MDCK Permeability:  3.234400355722755e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.03
30% Bioavailability (F30%):  0.059

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.136
Plasma Protein Binding (PPB):  87.09573364257812%
Volume Distribution (VD):  1.49
Pgp-substrate:  9.72645092010498%

ADMET: Metabolism

CYP1A2-inhibitor:  0.919
CYP1A2-substrate:  0.21
CYP2C19-inhibitor:  0.612
CYP2C19-substrate:  0.673
CYP2C9-inhibitor:  0.345
CYP2C9-substrate:  0.089
CYP2D6-inhibitor:  0.48
CYP2D6-substrate:  0.255
CYP3A4-inhibitor:  0.723
CYP3A4-substrate:  0.238

ADMET: Excretion

Clearance (CL):  14.639
Half-life (T1/2):  0.102

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.124
Drug-inuced Liver Injury (DILI):  0.326
AMES Toxicity:  0.159
Rat Oral Acute Toxicity:  0.921
Maximum Recommended Daily Dose:  0.733
Skin Sensitization:  0.855
Carcinogencity:  0.903
Eye Corrosion:  0.941
Eye Irritation:  0.972
Respiratory Toxicity:  0.97

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

  Natural Product: NPC134717

Natural Product ID:  NPC134717
Common Name*:   RJIIQBYZGJSODH-QWRGUYRKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RJIIQBYZGJSODH-QWRGUYRKSA-N
Standard InCHI:  InChI=1S/C14H16N2O6/c17-12(18)9-6-8(7-10(15-9)13(19)20)3-5-16-4-1-2-11(16)14(21)22/h3,5-6,10-11H,1-2,4,7H2,(H3,17,18,19,20,21,22)/t10-,11-/m0/s1
SMILES:  C1C[C@@H](C(=O)O)[N+](=CC=C2C=C(C(=O)[O-])N[C@@H](C2)C(=O)O)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6096870
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:0004322] Proline and derivatives

*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
NPO13512 Opuntia ficus-indica Species Cactaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.indcrop.2014.08.046]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. PMID[11277746]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[11678654]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15787451]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota Roots Anhui, China n.a. PMID[22694318]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30326 Polygonum perfoliatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13512 Opuntia ficus-indica Species Cactaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13512 Opuntia ficus-indica Species Cactaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13512 Opuntia ficus-indica Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7507 Portulaca grandiflora Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae 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
NPT492 Cell Line Caco-2 Homo sapiens IC50 = 115000.0 nM PMID[494480]
NPT169 Cell Line B16-F10 Mus musculus Inhibition = 42.0 % PMID[494480]
NPT169 Cell Line B16-F10 Mus musculus Inhibition = 83.0 % PMID[494480]
NPT169 Cell Line B16-F10 Mus musculus Inhibition = 86.0 % PMID[494480]
NPT737 Cell Line HUVEC Homo sapiens Inhibition = -15.0 % PMID[494480]
NPT27 Others Unspecified Ct = 0.05 ng/mg PMID[494480]
NPT27 Others Unspecified Ct = 0.09 ng/mg PMID[494480]
NPT27 Others Unspecified Cp = 0.2 uM/g PMID[494480]
NPT27 Others Unspecified Ct = 20.0 ng/g PMID[494480]
NPT2 Others Unspecified Bmax = 0.52 nmol PMID[494480]

☑ 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 NPC134717 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

  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 NPC134717 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

  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