Structure

Physi-Chem Properties

Molecular Weight:  148.05
Volume:  129.622
LogP:  -2.412
LogD:  -2.186
LogS:  -0.186
# Rotatable Bonds:  3
TPSA:  126.64
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.246
Synthetic Accessibility Score:  3.471
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:  -5.943
MDCK Permeability:  0.007819443009793758
Pgp-inhibitor:  0.002
Pgp-substrate:  0.277
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.163

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.678
Plasma Protein Binding (PPB):  12.622770309448242%
Volume Distribution (VD):  0.334
Pgp-substrate:  85.21160125732422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.044
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.036
CYP2D6-substrate:  0.169
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.072

ADMET: Excretion

Clearance (CL):  1.852
Half-life (T1/2):  0.602

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.099
Drug-inuced Liver Injury (DILI):  0.172
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.242
Carcinogencity:  0.016
Eye Corrosion:  0.003
Eye Irritation:  0.029
Respiratory Toxicity:  0.272

Download Data

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

  Natural Product: NPC283312

Natural Product ID:  NPC283312
Common Name*:   VQTLPSCRBFYDNX-LWMBPPNESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VQTLPSCRBFYDNX-LWMBPPNESA-N
Standard InCHI:  InChI=1S/C4H8N2O4/c5-1(4(9)10)2(7)3(6)8/h1-2,7H,5H2,(H2,6,8)(H,9,10)/t1-,2-/m0/s1
SMILES:  [C@H]([C@@H](C(=N)O)O)(C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15991574
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:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004312] Asparagine 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
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota Fruits n.a. n.a. PMID[10757716]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota roots n.a. n.a. PMID[20346658]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[23439553]
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota n.a. Tibet, China n.a. PMID[24645629]
NPO18155 Salvia argentea Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[25880372]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. tuber n.a. Database[Article]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18155 Salvia argentea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9176 Peridinium balticum Species Peridiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9261 Ophiopogon japonicus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26394 Sarcodon leucopus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1574 Penstemon cyathophorus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16797 Polyangium fumosum Species Polyangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6078 Arthrinium phaeospermum Species Apiosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10357 Krameria sonorae Species Krameriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2156 Parkia bicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14709 Senecio brevilorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15307 Entandrophragma delevoyi Species Meliaceae 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 NPC283312 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 NPC283312 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