Structure

Physi-Chem Properties

Molecular Weight:  150.02
Volume:  125.209
LogP:  -1.786
LogD:  -1.578
LogS:  -0.439
# Rotatable Bonds:  3
TPSA:  115.06
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.248
Synthetic Accessibility Score:  3.397
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.677
MDCK Permeability:  0.008829768747091293
Pgp-inhibitor:  0.0
Pgp-substrate:  0.058
Human Intestinal Absorption (HIA):  0.7
20% Bioavailability (F20%):  0.959
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.662
Plasma Protein Binding (PPB):  14.344491958618164%
Volume Distribution (VD):  0.268
Pgp-substrate:  78.6502685546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.048
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.077
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.044
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.103
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.021

ADMET: Excretion

Clearance (CL):  1.498
Half-life (T1/2):  0.775

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.047
Drug-inuced Liver Injury (DILI):  0.455
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.741
Carcinogencity:  0.005
Eye Corrosion:  0.005
Eye Irritation:  0.991
Respiratory Toxicity:  0.888

Download Data

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

  Natural Product: NPC185339

Natural Product ID:  NPC185339
Common Name*:   XPQGQRUKEBSKNW-OLXYHTOASA-M
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XPQGQRUKEBSKNW-OLXYHTOASA-M
Standard InCHI:  InChI=1S/C4H6O6.CH2O3.Na/c5-1(3(7)8)2(6)4(9)10;2-1(3)4;/h1-2,5-6H,(H,7,8)(H,9,10);(H2,2,3,4);/q;;+1/p-1/t1-,2-;;/m1../s1
SMILES:  [C@@H]([C@H](C(=O)O)O)(C(=O)[O-])O.C(=O)(O)O.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24848123
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000215] Sugar acids 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
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO23680 Ficus pumila Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17086 Hibiscus rosa-sinensis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30421 Codonopsis tangshen Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23680 Ficus pumila Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17086 Hibiscus rosa-sinensis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30421 Codonopsis tangshen Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17086 Hibiscus rosa-sinensis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23680 Ficus pumila Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23680 Ficus pumila Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17086 Hibiscus rosa-sinensis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12328 Ampelopsis japonica Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22659 Codonopsis subglobosa Species Campanulaceae 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 NPC185339 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 NPC185339 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