Structure

Physi-Chem Properties

Molecular Weight:  164.06
Volume:  164.76
LogP:  -0.07
LogD:  -0.065
LogS:  -1.428
# Rotatable Bonds:  1
TPSA:  55.02
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.598
Synthetic Accessibility Score:  2.53
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:  -4.624
MDCK Permeability:  2.6720530513557605e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.078
30% Bioavailability (F30%):  0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.959
Plasma Protein Binding (PPB):  31.485820770263672%
Volume Distribution (VD):  0.847
Pgp-substrate:  64.77705383300781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.282
CYP1A2-substrate:  0.942
CYP2C19-inhibitor:  0.129
CYP2C19-substrate:  0.53
CYP2C9-inhibitor:  0.063
CYP2C9-substrate:  0.707
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.492
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.283

ADMET: Excretion

Clearance (CL):  6.648
Half-life (T1/2):  0.793

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.936
Drug-inuced Liver Injury (DILI):  0.424
AMES Toxicity:  0.388
Rat Oral Acute Toxicity:  0.934
Maximum Recommended Daily Dose:  0.083
Skin Sensitization:  0.141
Carcinogencity:  0.48
Eye Corrosion:  0.529
Eye Irritation:  0.9
Respiratory Toxicity:  0.568

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

  Natural Product: NPC78625

Natural Product ID:  NPC78625
Common Name*:   Ricinine
IUPAC Name:   4-methoxy-1-methyl-2-oxopyridine-3-carbonitrile
Synonyms:  
Standard InCHIKey:  PETSAYFQSGAEQY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H8N2O2/c1-10-4-3-7(12-2)6(5-9)8(10)11/h3-4H,1-2H3
SMILES:  N#Cc1c(OC)ccn(c1=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1329957
PubChem CID:   10666
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0003972] 3-pyridinecarbonitriles

*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
NPO17682 Lamellodysidea chlorea Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[15332844]
NPO11403 Bussea sakalava Species Fabaceae Eukaryota n.a. root n.a. PMID[20942441]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[26509914]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11403 Bussea sakalava Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6383 Lepisanthes tetraphylla Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16922 Xenia viridis Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15912 Cheimonophyllum candidissimum Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1712 Tetragonotheca repanda Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11670 Stomozoa murrayi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17682 Lamellodysidea chlorea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18072 Coespeletia moritziana Species Asteraceae 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
NPT483 Individual Protein Prelamin-A/C Homo sapiens Potency = 1778.3 nM PMID[449013]
NPT51 Individual Protein Microtubule-associated protein tau Homo sapiens Potency = 25118.9 nM PMID[449014]
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Potency = 12589.3 nM PMID[449015]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens Potency = 12589.3 nM PMID[449013]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 3162.3 nM PMID[449016]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 5.2 nM PMID[449016]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 21136.0 nM PMID[449017]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 18837.5 nM PMID[449017]
NPT27 Others Unspecified LD50 = 80.0 mg.kg-1 PMID[449012]
NPT29 Organism Rattus norvegicus Rattus norvegicus ED = 6.0 mg kg-1 PMID[449012]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 11689.1 nM PMID[449016]
NPT8 Individual Protein DNA polymerase iota Homo sapiens Potency n.a. 79432.8 nM PMID[449016]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 4653.5 nM PMID[449016]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[449019]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[449019]

☑ 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 NPC78625 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
0.6456 Remote Similarity NPC201332
0.6 Remote Similarity NPC252503
0.5946 Remote Similarity NPC270412
0.5946 Remote Similarity NPC14437
0.573 Remote Similarity NPC296589
0.5632 Remote Similarity NPC312419
0.5625 Remote Similarity NPC477688
0.561 Remote Similarity NPC326126

  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 NPC78625 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
0.5946 Remote Similarity NPD9418 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