Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  257.45
LogP:  4.855
LogD:  4.304
LogS:  -5.016
# Rotatable Bonds:  6
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.412
Synthetic Accessibility Score:  3.162
Fsp3:  0.467
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.576
MDCK Permeability:  2.5412948161829263e-05
Pgp-inhibitor:  0.102
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.082
30% Bioavailability (F30%):  0.037

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.774
Plasma Protein Binding (PPB):  98.73790740966797%
Volume Distribution (VD):  3.65
Pgp-substrate:  1.940216302871704%

ADMET: Metabolism

CYP1A2-inhibitor:  0.881
CYP1A2-substrate:  0.484
CYP2C19-inhibitor:  0.472
CYP2C19-substrate:  0.832
CYP2C9-inhibitor:  0.402
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.434
CYP2D6-substrate:  0.697
CYP3A4-inhibitor:  0.242
CYP3A4-substrate:  0.236

ADMET: Excretion

Clearance (CL):  8.891
Half-life (T1/2):  0.477

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.69
Drug-inuced Liver Injury (DILI):  0.015
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.649
Skin Sensitization:  0.953
Carcinogencity:  0.181
Eye Corrosion:  0.968
Eye Irritation:  0.986
Respiratory Toxicity:  0.418

Download Data

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

  Natural Product: NPC60250

Natural Product ID:  NPC60250
Common Name*:   (3E)-3-Hydroxyiminobutan-2-One
IUPAC Name:   (3E)-3-hydroxyiminobutan-2-one
Synonyms:   2,3-Butanedione Monoxime
Standard InCHIKey:  FSEUPUDHEBLWJY-HWKANZROSA-N
Standard InCHI:  InChI=1S/C4H7NO2/c1-3(5-7)4(2)6/h7H,1-2H3/b5-3+
SMILES:  C/C(=NO)/C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1255578
PubChem CID:   6409633
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0000411] Oximes
          • [CHEMONTID:0003079] Ketoximes

*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
NPO10597 Fructus syzygii n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO10597 Fructus syzygii n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT46 Individual Protein Thyroid hormone receptor beta-1 Homo sapiens Potency = 125.9 nM PMID[492323]
NPT58 Individual Protein Bloom syndrome protein Homo sapiens Potency = 2.8 nM PMID[492323]
NPT1416 Individual Protein Neuropeptide S receptor Homo sapiens Potency = 31622.8 nM PMID[492323]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 35481.3 nM PMID[492322]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 597.3 nM PMID[492322]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 3661.1 nM PMID[492322]
NPT104 Individual Protein Cerebroside-sulfatase Homo sapiens Potency n.a. 1069.1 nM PMID[492322]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens Kd = 392600.0 nM PMID[492326]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens max activation = 20.0 % PMID[492326]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Potency = 20596.2 nM PMID[492322]
NPT796 Individual Protein Peripheral myelin protein 22 Homo sapiens Potency = 84921.4 nM PMID[492323]
NPT755 Individual Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 Homo sapiens Potency n.a. 75.7 nM PMID[492322]
NPT7 Individual Protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus Potency n.a. 2238.7 nM PMID[492322]
NPT2 Others Unspecified Potency n.a. 89.1 nM PMID[492324]
NPT2 Others Unspecified Potency n.a. 89.1 nM PMID[492323]
NPT2 Others Unspecified Potency n.a. 89.1 nM PMID[492325]
NPT35 Others n.a. pKa = 9.5 n.a. PMID[492326]
NPT35 Others n.a. LogP = 0.48 n.a. PMID[492326]

☑ 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 NPC60250 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
0.6333 Remote Similarity NPC319972
0.6098 Remote Similarity NPC235432
0.5882 Remote Similarity NPC290188
0.5862 Remote Similarity NPC171188

  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 NPC60250 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
0.6333 Remote Similarity NPD7369 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