Structure

Physi-Chem Properties

Molecular Weight:  217.07
Volume:  220.544
LogP:  0.774
LogD:  0.728
LogS:  -2.246
# Rotatable Bonds:  2
TPSA:  55.73
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.653
Synthetic Accessibility Score:  4.68
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.622
MDCK Permeability:  1.824002538342029e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.044
20% Bioavailability (F20%):  0.92
30% Bioavailability (F30%):  0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.996
Plasma Protein Binding (PPB):  69.9527816772461%
Volume Distribution (VD):  0.642
Pgp-substrate:  36.301780700683594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.471
CYP1A2-substrate:  0.237
CYP2C19-inhibitor:  0.119
CYP2C19-substrate:  0.763
CYP2C9-inhibitor:  0.052
CYP2C9-substrate:  0.591
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.631
CYP3A4-inhibitor:  0.071
CYP3A4-substrate:  0.251

ADMET: Excretion

Clearance (CL):  1.814
Half-life (T1/2):  0.551

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.552
Drug-inuced Liver Injury (DILI):  0.363
AMES Toxicity:  0.966
Rat Oral Acute Toxicity:  0.915
Maximum Recommended Daily Dose:  0.897
Skin Sensitization:  0.917
Carcinogencity:  0.853
Eye Corrosion:  0.057
Eye Irritation:  0.371
Respiratory Toxicity:  0.922

Download Data

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

  Natural Product: NPC263266

Natural Product ID:  NPC263266
Common Name*:   Vermelhotin
IUPAC Name:   (3Z)-3-[6-[(E)-prop-1-enyl]pyran-2-ylidene]pyrrolidine-2,4-dione
Synonyms:  
Standard InCHIKey:  AGPWDHWZOCXKTC-ZSLCMEJMSA-N
Standard InCHI:  InChI=1S/C12H11NO3/c1-2-4-8-5-3-6-10(16-8)11-9(14)7-13-12(11)15/h2-6H,7H2,1H3,(H,13,15)/b4-2+,11-10-
SMILES:  C/C=C/C1=CC=C/C(=C/2C(=O)CN=C2O)/O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2426307
PubChem CID:   73349254
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans

*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
NPO32874 unidentified marine-derived fungus cri247-01 Species n.a. n.a. n.a. n.a. n.a. Database[Title]

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus FC = 13.72 n.a. PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus FC = 144.02 n.a. PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus FC = 203.39 n.a. PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition > 95.0 % PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus Survival > 80.0 % PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 5350.0 nM PMID[533710]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition >= 80.0 % PMID[533710]
NPT171 Cell Line MRC5 Homo sapiens IC50 = 6.97 ug.mL-1 PMID[533711]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 6.2 ug.mL-1 PMID[533711]
NPT115 Organism Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Ra MIC = 3.1 ug.mL-1 PMID[533711]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 3.1 ug.mL-1 PMID[533711]

☑ 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 NPC263266 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
0.7527 Intermediate Similarity NPC313234
0.734 Intermediate Similarity NPC175531
0.7215 Intermediate Similarity NPC469836
0.7037 Intermediate Similarity NPC469835
0.6875 Remote Similarity NPC4706
0.6832 Remote Similarity NPC24389
0.6622 Remote Similarity NPC245650
0.6438 Remote Similarity NPC218486
0.6404 Remote Similarity NPC469838
0.6404 Remote Similarity NPC469833
0.6329 Remote Similarity NPC475618
0.6316 Remote Similarity NPC189700
0.625 Remote Similarity NPC471565
0.625 Remote Similarity NPC471566
0.6154 Remote Similarity NPC6795
0.6154 Remote Similarity NPC130953
0.6145 Remote Similarity NPC471022
0.6053 Remote Similarity NPC150717
0.6053 Remote Similarity NPC221763
0.6049 Remote Similarity NPC471556
0.6026 Remote Similarity NPC133600
0.6022 Remote Similarity NPC185928
0.6 Remote Similarity NPC2328
0.6 Remote Similarity NPC77891
0.5949 Remote Similarity NPC98519
0.5946 Remote Similarity NPC191643
0.593 Remote Similarity NPC326126
0.5921 Remote Similarity NPC173157
0.5921 Remote Similarity NPC25038
0.5904 Remote Similarity NPC470442
0.59 Remote Similarity NPC175614
0.5875 Remote Similarity NPC273614
0.5854 Remote Similarity NPC476589
0.5802 Remote Similarity NPC473737
0.5789 Remote Similarity NPC14234
0.5789 Remote Similarity NPC184014
0.5789 Remote Similarity NPC132669
0.5789 Remote Similarity NPC269800
0.5789 Remote Similarity NPC246519
0.5789 Remote Similarity NPC44193
0.5783 Remote Similarity NPC187315
0.5783 Remote Similarity NPC315115
0.5769 Remote Similarity NPC469598
0.5769 Remote Similarity NPC474825
0.5765 Remote Similarity NPC473277
0.5753 Remote Similarity NPC234084
0.5753 Remote Similarity NPC126184
0.5739 Remote Similarity NPC469515
0.573 Remote Similarity NPC470705
0.5714 Remote Similarity NPC313911
0.5714 Remote Similarity NPC314854
0.57 Remote Similarity NPC116930
0.5698 Remote Similarity NPC59558
0.5698 Remote Similarity NPC315597
0.5686 Remote Similarity NPC167380
0.5686 Remote Similarity NPC265662
0.5684 Remote Similarity NPC296589
0.5676 Remote Similarity NPC307435
0.5676 Remote Similarity NPC267692
0.5664 Remote Similarity NPC476190
0.5647 Remote Similarity NPC313444
0.5647 Remote Similarity NPC249713
0.5647 Remote Similarity NPC287705
0.5647 Remote Similarity NPC477117
0.5641 Remote Similarity NPC51846
0.5638 Remote Similarity NPC475083
0.5636 Remote Similarity NPC170375
0.5616 Remote Similarity NPC128520
0.561 Remote Similarity NPC475073
0.561 Remote Similarity NPC471023
0.56 Remote Similarity NPC267340
0.56 Remote Similarity NPC304223
0.56 Remote Similarity NPC145032
0.56 Remote Similarity NPC54542
0.56 Remote Similarity NPC243539

  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 NPC263266 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
0.5806 Remote Similarity NPD205 Approved
0.5636 Remote Similarity NPD7601 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