Structure

Physi-Chem Properties

Molecular Weight:  332.07
Volume:  293.648
LogP:  -0.51
LogD:  -0.226
LogS:  -1.234
# Rotatable Bonds:  4
TPSA:  166.14
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  2
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.279
Synthetic Accessibility Score:  3.819
Fsp3:  0.462
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.416
MDCK Permeability:  3.246457708883099e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.3
Human Intestinal Absorption (HIA):  0.781
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.26
Plasma Protein Binding (PPB):  78.1203842163086%
Volume Distribution (VD):  0.403
Pgp-substrate:  27.990678787231445%

ADMET: Metabolism

CYP1A2-inhibitor:  0.047
CYP1A2-substrate:  0.065
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.095
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.143
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.014

ADMET: Excretion

Clearance (CL):  2.762
Half-life (T1/2):  0.931

ADMET: Toxicity

hERG Blockers:  0.071
Human Hepatotoxicity (H-HT):  0.019
Drug-inuced Liver Injury (DILI):  0.765
AMES Toxicity:  0.341
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.853
Carcinogencity:  0.03
Eye Corrosion:  0.004
Eye Irritation:  0.426
Respiratory Toxicity:  0.026

Download Data

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

  Natural Product: NPC2458

Natural Product ID:  NPC2458
Common Name*:   KGHSLXLLBHRMML-PHSPRSPYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KGHSLXLLBHRMML-PHSPRSPYSA-N
Standard InCHI:  InChI=1S/C13H16O10/c1-21-12-9(18)8(17)10(19)13(23-12)22-11(20)4-2-5(14)7(16)6(15)3-4/h2-3,8-10,12-19H,1H3/t8-,9-,10+,12-,13?/m0/s1
SMILES:  CO[C@@H]1[C@H]([C@@H]([C@H](C(OC(=O)c2cc(c(c(c2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   124375
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0001248] Hydroxybenzoic acid derivatives
            • [CHEMONTID:0001251] Gallic acid and derivatives
              • [CHEMONTID:0003539] Galloyl esters

*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
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. fruit n.a. DOI[10.1007/s00217-007-0799-1]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. flower n.a. DOI[10.1016/j.foodchem.2011.01.077]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[11754604]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seeds n.a. n.a. PMID[15620261]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota Roots Simao city, Yunnan Province, China 2007-MAY PMID[19374435]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Root Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Twig n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11632 Fructus phyllanthi n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11632 Fructus phyllanthi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25238 Rheum coreanum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25238 Rheum coreanum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28450 Phyllanthus emblica Species Phyllanthaceae 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

☑ 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 NPC2458 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 NPC2458 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