Structure

Physi-Chem Properties

Molecular Weight:  326.06
Volume:  296.881
LogP:  -0.15
LogD:  0.351
LogS:  -1.236
# Rotatable Bonds:  4
TPSA:  164.75
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.316
Synthetic Accessibility Score:  3.758
Fsp3:  0.286
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:  -6.218
MDCK Permeability:  1.1300216101517435e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.822
20% Bioavailability (F20%):  0.93
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.25
Plasma Protein Binding (PPB):  74.74845123291016%
Volume Distribution (VD):  0.453
Pgp-substrate:  21.492267608642578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.217
CYP1A2-substrate:  0.019
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.04
CYP2C9-inhibitor:  0.16
CYP2C9-substrate:  0.1
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.118
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.016

ADMET: Excretion

Clearance (CL):  8.004
Half-life (T1/2):  0.964

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.283
Drug-inuced Liver Injury (DILI):  0.687
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.198
Skin Sensitization:  0.697
Carcinogencity:  0.072
Eye Corrosion:  0.004
Eye Irritation:  0.158
Respiratory Toxicity:  0.078

Download Data

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

  Natural Product: NPC212628

Natural Product ID:  NPC212628
Common Name*:   CFCRCJAHPCJZLP-FOGDFJRCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CFCRCJAHPCJZLP-FOGDFJRCSA-N
Standard InCHI:  InChI=1S/C14H14O9/c15-7-2-6(3-8(16)11(7)18)14(22)23-10-4-5(13(20)21)1-9(17)12(10)19/h2-4,9-10,12,15-19H,1H2,(H,20,21)/t9-,10-,12+/m1/s1
SMILES:  C1C(=C[C@H]([C@H]([C@@H]1O)O)OC(=O)c1cc(c(c(c1)O)O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10449030
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
NPO6039 Aglaia laxiflora Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[10785416]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. PMID[11223086]
NPO9973 Euphorbia turczaninowii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[11520228]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. PMID[14559084]
NPO7381 Ircinia spinosula Species Irciniidae Eukaryota n.a. Bay of Naples, Italy n.a. PMID[7714539]
NPO7690 Nyssa sinensis Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7690 Nyssa sinensis Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9207 Styrax ferrugineus Species Styracaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21977 Psora corallina Species Psoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20026 Senecio callosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8437 Encyothalia cliftonii Species Sporochnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7381 Ircinia spinosula Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22543 Cleome chrysantha Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2174 Polysiphonia elongata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7625 Scopolia hladnikiana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8848 Colubrina elliptica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7292 Excoecaria kawakamii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7862 Faramea cyanea Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7013 Dicoma capensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7690 Nyssa sinensis Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5301 Haplophyllum ferganicum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1496 Stevia porphyrea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4073 Geranium sylvaticum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3924 Penicillium alutaceum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9757 Cladonia macilenta Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO550 Callicarpa maingayi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8313 Rhipocephalus phoenix Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2461 Perilla acuta Species Araneidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26170 Haliclona mucosa Species Chalinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15448 Chrysothamnus parryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6039 Aglaia laxiflora Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9973 Euphorbia turczaninowii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5541 Crotalaria aegyptiaca Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8909 Pteris radiata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2723 Artemisia carvifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3119 Cephalaria uralensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8773 Sonchus ortunoi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO762 Digitalis isabelliana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9207 Styrax ferrugineus Species Styracaceae 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 NPC212628 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 NPC212628 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