Structure

Physi-Chem Properties

Molecular Weight:  167.06
Volume:  165.189
LogP:  0.325
LogD:  0.083
LogS:  -1.546
# Rotatable Bonds:  1
TPSA:  74.29
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.613
Synthetic Accessibility Score:  2.969
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:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.046
MDCK Permeability:  0.0002328664413653314
Pgp-inhibitor:  0.0
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.088
20% Bioavailability (F20%):  0.106
30% Bioavailability (F30%):  0.867

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.422
Plasma Protein Binding (PPB):  59.64220428466797%
Volume Distribution (VD):  1.117
Pgp-substrate:  61.16543960571289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.452
CYP1A2-substrate:  0.769
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.255
CYP2C9-inhibitor:  0.084
CYP2C9-substrate:  0.737
CYP2D6-inhibitor:  0.183
CYP2D6-substrate:  0.665
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  1.6
Half-life (T1/2):  0.567

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.321
Drug-inuced Liver Injury (DILI):  0.84
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.155
Maximum Recommended Daily Dose:  0.094
Skin Sensitization:  0.429
Carcinogencity:  0.053
Eye Corrosion:  0.353
Eye Irritation:  0.939
Respiratory Toxicity:  0.58

Download Data

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

  Natural Product: NPC470442

Natural Product ID:  NPC470442
Common Name*:   (3Z)-3-(1-Aminoethylidene)-6-Methylpyran-2,4-Dione
IUPAC Name:   (3Z)-3-(1-aminoethylidene)-6-methylpyran-2,4-dione
Synonyms:  
Standard InCHIKey:  ONMOQSQBAAMLAG-ALCCZGGFSA-N
Standard InCHI:  InChI=1S/C8H9NO3/c1-4-3-6(10)7(5(2)9)8(11)12-4/h3H,9H2,1-2H3/b7-5-
SMILES:  CC1=CC(=O)/C(=C(/N)C)/C(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2036495
PubChem CID:   5710126
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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
NPO24024 Fusarium semitectum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[10978211]
NPO24024 Fusarium semitectum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[22439674]
NPO24024 Fusarium semitectum Species Nectriaceae 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
NPT111 Cell Line K562 Homo sapiens GI50 = 9000.0 nM PMID[541916]
NPT737 Cell Line HUVEC Homo sapiens GI50 = 68200.0 nM PMID[541916]
NPT165 Cell Line HeLa Homo sapiens CC50 = 103600.0 nM PMID[541916]

☑ 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 NPC470442 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
0.7121 Intermediate Similarity NPC173157
0.6923 Remote Similarity NPC191643
0.6765 Remote Similarity NPC150717
0.6765 Remote Similarity NPC221763
0.6719 Remote Similarity NPC234084
0.6716 Remote Similarity NPC218486
0.6667 Remote Similarity NPC477117
0.6486 Remote Similarity NPC476589
0.6479 Remote Similarity NPC133600
0.6438 Remote Similarity NPC2328
0.641 Remote Similarity NPC133098
0.6395 Remote Similarity NPC296589
0.6389 Remote Similarity NPC309408
0.6389 Remote Similarity NPC79756
0.6377 Remote Similarity NPC25038
0.6286 Remote Similarity NPC86948
0.6267 Remote Similarity NPC471565
0.6267 Remote Similarity NPC471556
0.6267 Remote Similarity NPC471566
0.6216 Remote Similarity NPC132243
0.6212 Remote Similarity NPC135698
0.6184 Remote Similarity NPC315115
0.6154 Remote Similarity NPC473277
0.6119 Remote Similarity NPC236338
0.6081 Remote Similarity NPC151648
0.6081 Remote Similarity NPC15193
0.6076 Remote Similarity NPC315199
0.6053 Remote Similarity NPC112312
0.6026 Remote Similarity NPC313444
0.6 Remote Similarity NPC270706
0.597 Remote Similarity NPC126184
0.5946 Remote Similarity NPC429928
0.5942 Remote Similarity NPC151919
0.5909 Remote Similarity NPC128280
0.5904 Remote Similarity NPC263266
0.5904 Remote Similarity NPC470705
0.5897 Remote Similarity NPC203335
0.589 Remote Similarity NPC189700
0.5882 Remote Similarity NPC275316
0.5882 Remote Similarity NPC27264
0.5882 Remote Similarity NPC15789
0.5875 Remote Similarity NPC316029
0.5875 Remote Similarity NPC315285
0.5875 Remote Similarity NPC315597
0.5867 Remote Similarity NPC270412
0.5867 Remote Similarity NPC14437
0.5867 Remote Similarity NPC263732
0.5844 Remote Similarity NPC131174
0.5844 Remote Similarity NPC470688
0.5843 Remote Similarity NPC281172
0.5833 Remote Similarity NPC316324
0.5823 Remote Similarity NPC287705
0.5811 Remote Similarity NPC86789
0.5811 Remote Similarity NPC203233
0.5811 Remote Similarity NPC286189
0.5797 Remote Similarity NPC148056
0.5789 Remote Similarity NPC475073
0.5789 Remote Similarity NPC474658
0.5784 Remote Similarity NPC220730
0.5778 Remote Similarity NPC291712
0.5769 Remote Similarity NPC475555
0.5769 Remote Similarity NPC475675
0.5769 Remote Similarity NPC470033
0.5758 Remote Similarity NPC26600
0.5758 Remote Similarity NPC47946
0.5735 Remote Similarity NPC15912
0.5733 Remote Similarity NPC130953
0.5732 Remote Similarity NPC287878
0.5714 Remote Similarity NPC475618
0.5714 Remote Similarity NPC66789
0.5696 Remote Similarity NPC132286
0.5694 Remote Similarity NPC478117
0.5679 Remote Similarity NPC59558
0.5679 Remote Similarity NPC202011
0.5672 Remote Similarity NPC197467
0.5652 Remote Similarity NPC220191
0.5647 Remote Similarity NPC471225
0.5641 Remote Similarity NPC273600
0.5641 Remote Similarity NPC133904
0.5641 Remote Similarity NPC220766
0.5641 Remote Similarity NPC182794
0.5634 Remote Similarity NPC474805
0.5625 Remote Similarity NPC470256
0.5625 Remote Similarity NPC79220
0.5625 Remote Similarity NPC280374
0.5625 Remote Similarity NPC238223
0.56 Remote Similarity NPC159650
0.56 Remote Similarity NPC22897

  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 NPC470442 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
0.6029 Remote Similarity NPD6927 Phase 3
0.5867 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5696 Remote Similarity NPD3709 Clinical (unspecified phase)

  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