Structure

Physi-Chem Properties

Molecular Weight:  190.01
Volume:  157.398
LogP:  -0.162
LogD:  -0.123
LogS:  -0.737
# Rotatable Bonds:  2
TPSA:  110.13
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.515
Synthetic Accessibility Score:  3.946
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.829
MDCK Permeability:  0.0006788293831050396
Pgp-inhibitor:  0.0
Pgp-substrate:  0.02
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.756
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.416
Plasma Protein Binding (PPB):  16.043781280517578%
Volume Distribution (VD):  0.262
Pgp-substrate:  70.95916748046875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.085
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.048
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.746
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.115
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.033

ADMET: Excretion

Clearance (CL):  5.645
Half-life (T1/2):  0.764

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.04
Drug-inuced Liver Injury (DILI):  0.345
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.077
Skin Sensitization:  0.324
Carcinogencity:  0.031
Eye Corrosion:  0.994
Eye Irritation:  0.97
Respiratory Toxicity:  0.042

Download Data

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

  Natural Product: NPC1042

Natural Product ID:  NPC1042
Common Name*:   WCPDBYPYIAOHBP-LURJTMIESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WCPDBYPYIAOHBP-LURJTMIESA-N
Standard InCHI:  InChI=1S/C6H6O7/c7-3(8)1-6(11)2-4(9)12-13-5(6)10/h11H,1-2H2,(H,7,8)/t6-/m0/s1
SMILES:  C(C(=O)O)[C@@]1(CC(=O)OOC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   54759166
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001986] Tricarboxylic 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
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1021/jf970571j]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. seed n.a. PMID[10898633]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[11076555]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[11459643]
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]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[1517743]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. fruit n.a. PMID[240326]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24211545]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
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]
NPO12323 Bos taurus Species Bovidae Eukaryota Urine n.a. n.a. PMID[6330305]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[8277318]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[932730]
NPO366 Pyrus communis Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota 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 Fruits n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO27580 Pedicellus melo n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO16230 Malus pumila 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]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21919 Polysaccharidum versicolor n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30615 Fructus vitis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota 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]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23604 Fructus choerospondiatis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume 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]
NPO23448 Vinegar n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO27580 Pedicellus melo n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10226 Fructus vitis viniferae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO26356 Radix vitis romanetii Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24837 Radix glycyrrhizae uralensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6117 Poria Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23604 Fructus choerospondiatis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26241 Herba fragariae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO21919 Polysaccharidum versicolor n.a. n.a. n.a. 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]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11391 Polygonum cuspidatum Species Polygonaceae 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]
NPO17393 Bubalus bubalis Species Bovidae 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]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11391 Polygonum cuspidatum Species Polygonaceae 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]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26327 Chaenomeles sinensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[USDA]

☑ 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 NPC1042 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 NPC1042 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