Structure

Physi-Chem Properties

Molecular Weight:  117.04
Volume:  109.835
LogP:  -2.791
LogD:  -1.272
LogS:  -0.667
# Rotatable Bonds:  3
TPSA:  80.39
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.464
Synthetic Accessibility Score:  3.369
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:  -6.015
MDCK Permeability:  0.005284853279590607
Pgp-inhibitor:  0.001
Pgp-substrate:  0.05
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.08
Plasma Protein Binding (PPB):  31.310375213623047%
Volume Distribution (VD):  0.554
Pgp-substrate:  79.15544128417969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.05
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.582
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.16
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.05

ADMET: Excretion

Clearance (CL):  7.604
Half-life (T1/2):  0.774

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.439
Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.913
Carcinogencity:  0.038
Eye Corrosion:  0.486
Eye Irritation:  0.251
Respiratory Toxicity:  0.185

Download Data

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

  Natural Product: NPC57429

Natural Product ID:  NPC57429
Common Name*:   CGJJPOYORMGCGE-VKHMYHEASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CGJJPOYORMGCGE-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C4H7NO3/c5-3(2-6)1-4(7)8/h2-3H,1,5H2,(H,7,8)/t3-/m0/s1
SMILES:  C([C@@H](C=O)N)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6540254
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0001878] Beta amino 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
NPO9935 Polygonatum sibiricum Species Asparagaceae Eukaryota rhizomes Kangwon Province of Korea 2002-MAY PMID[16562835]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. PMID[27439360]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31566 Massa fermentata n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO9935 Polygonatum sibiricum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29997 Colla carapacis Species Bombycidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15987 Plastrum testudinis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17349 Colla carapacis et plastri testudinis Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23234 Ageratum conyzoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9935 Polygonatum sibiricum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24062 Radix pseudostellariae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26323 Radix liriopes Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2831 Cornu saigae tataricae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO15987 Plastrum testudinis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO328 Plastrum testudinis praparata n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23234 Ageratum conyzoides Species Asteraceae 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]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9935 Polygonatum sibiricum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27364 Gallus gallus Species Phasianidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9935 Polygonatum sibiricum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23234 Ageratum conyzoides Species Asteraceae 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 NPC57429 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 NPC57429 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