Structure

Physi-Chem Properties

Molecular Weight:  114.02
Volume:  105.88
LogP:  -0.809
LogD:  -1.22
LogS:  -0.628
# Rotatable Bonds:  2
TPSA:  77.89
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.39
Synthetic Accessibility Score:  3.808
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.611
MDCK Permeability:  0.0017378866905346513
Pgp-inhibitor:  0.001
Pgp-substrate:  0.051
Human Intestinal Absorption (HIA):  0.897
20% Bioavailability (F20%):  0.329
30% Bioavailability (F30%):  0.129

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.958
Plasma Protein Binding (PPB):  40.1539306640625%
Volume Distribution (VD):  0.357
Pgp-substrate:  60.869895935058594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.336
CYP1A2-substrate:  0.521
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.08
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.446
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.276
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.134

ADMET: Excretion

Clearance (CL):  1.651
Half-life (T1/2):  0.705

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.789
Drug-inuced Liver Injury (DILI):  0.916
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.333
Carcinogencity:  0.012
Eye Corrosion:  0.952
Eye Irritation:  0.992
Respiratory Toxicity:  0.919

Download Data

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

  Natural Product: NPC36999

Natural Product ID:  NPC36999
Common Name*:   CPQNVDZMLDAKNR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CPQNVDZMLDAKNR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H4NO3/c1-2(6)3(5)4(7)8/h5H,1H3
SMILES:  CC(=O)C(=N)C(=O)[O]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   54732694
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000389] Keto acids and derivatives
        • [CHEMONTID:0001114] Beta-keto 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
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. seed n.a. PMID[10898633]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26343 Fagopyrum esculentum Species Polygonaceae 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]
NPO5939 Semen sojae praeparata n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15147 Ficus simplicissima Species Moraceae 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]
NPO16309 Semen astragali complanati n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO17349 Colla carapacis et plastri testudinis Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26323 Radix liriopes Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae 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]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae 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 NPC36999 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 NPC36999 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