Structure

Physi-Chem Properties

Molecular Weight:  198.08
Volume:  180.884
LogP:  -1.278
LogD:  -0.898
LogS:  -2.796
# Rotatable Bonds:  2
TPSA:  109.98
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  2.553
Fsp3:  0.286
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.5
MDCK Permeability:  0.00014719956379849464
Pgp-inhibitor:  0.001
Pgp-substrate:  0.962
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.029

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.627
Plasma Protein Binding (PPB):  18.482009887695312%
Volume Distribution (VD):  0.6
Pgp-substrate:  69.8635025024414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.485
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.126
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.116
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.225

ADMET: Excretion

Clearance (CL):  2.97
Half-life (T1/2):  0.842

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.315
Drug-inuced Liver Injury (DILI):  0.918
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.147
Carcinogencity:  0.015
Eye Corrosion:  0.003
Eye Irritation:  0.037
Respiratory Toxicity:  0.049

Download Data

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

  Natural Product: NPC326633

Natural Product ID:  NPC326633
Common Name*:   N-(6-Amino-3-Methyl-2,4-Dioxo-1H-Pyrimidin-5-Yl)Acetamide
IUPAC Name:   N-(6-amino-3-methyl-2,4-dioxo-1H-pyrimidin-5-yl)acetamide
Synonyms:  
Standard InCHIKey:  POQOTWQIYYNXAT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H10N4O3/c1-3(12)9-4-5(8)10-7(14)11(2)6(4)13/h8H2,1-2H3,(H,9,12)(H,10,14)
SMILES:  CC(=O)NC1=C(NC(=O)N(C1=O)C)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1899490
PubChem CID:   88299
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0003282] N-arylamides
          • [CHEMONTID:0004506] N-acetylarylamines

*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

☑ 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
NPT199 Individual Protein DNA polymerase kappa Homo sapiens Potency n.a. 751.9 nM PMID[475464]

☑ 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 NPC326633 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
0.5676 Remote Similarity NPC40598
0.5634 Remote Similarity NPC148178

  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 NPC326633 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
0.6026 Remote Similarity NPD1060 Clinical (unspecified phase)
0.5821 Remote Similarity NPD583 Approved
0.5821 Remote Similarity NPD584 Approved
0.5821 Remote Similarity NPD843 Clinical (unspecified phase)
0.5821 Remote Similarity NPD581 Approved
0.5652 Remote Similarity NPD562 Approved

  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