Structure

Physi-Chem Properties

Molecular Weight:  135.02
Volume:  116.419
LogP:  -1.688
LogD:  -1.459
LogS:  0.114
# Rotatable Bonds:  3
TPSA:  94.83
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.244
Synthetic Accessibility Score:  2.893
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:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.967
MDCK Permeability:  0.0074933660216629505
Pgp-inhibitor:  0.0
Pgp-substrate:  0.066
Human Intestinal Absorption (HIA):  0.969
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.642
Plasma Protein Binding (PPB):  16.82232093811035%
Volume Distribution (VD):  0.278
Pgp-substrate:  76.02873992919922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.392
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.132
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  3.028
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.16
Drug-inuced Liver Injury (DILI):  0.413
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.264
Carcinogencity:  0.013
Eye Corrosion:  0.019
Eye Irritation:  0.985
Respiratory Toxicity:  0.394

Download Data

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

  Natural Product: NPC51260

Natural Product ID:  NPC51260
Common Name*:   BJEPYKJPYRNKOW-DOCFYQGNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BJEPYKJPYRNKOW-DOCFYQGNSA-N
Standard InCHI:  InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1/i1+1
SMILES:  [13CH2]([C@H](C(=O)O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10953564
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0001713] Beta hydroxy 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]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[14600382]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20553004]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. calyx n.a. PMID[21561086]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota latex Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan Province, China 2011-Mar PMID[24033101]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. fruit n.a. PMID[24086493]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota trunk bark Yunnan, China n.a. PMID[24582402]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota Twigs n.a. n.a. PMID[25894905]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[26562741]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota Twigs n.a. n.a. PMID[28358502]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[29517238]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[31625751]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. Along the Valencian coast, Spain 2020-Jun&Jul PMID[35161358]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Herb n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2688 Pericarpium pyri n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO23628.1 Imperata cylindrica var. major Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24837 Radix glycyrrhizae uralensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23628.1 Imperata cylindrica var. major Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2688 Pericarpium pyri n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4640 Portulaca oleracea Species Portulacaceae 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]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18296 Diospyros kaki Species Ebenaceae 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]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17609 Thevetia neriifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8369 Antiaris toxicaria Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26327 Chaenomeles sinensis Species Rosaceae 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 NPC51260 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 NPC51260 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