Structure

Physi-Chem Properties

Molecular Weight:  222.17
Volume:  241.802
LogP:  -0.723
LogD:  0.709
LogS:  -0.621
# Rotatable Bonds:  2
TPSA:  23.55
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.677
Synthetic Accessibility Score:  3.339
Fsp3:  0.769
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:  -4.672
MDCK Permeability:  1.1746826203307137e-05
Pgp-inhibitor:  0.06
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.084
20% Bioavailability (F20%):  0.943
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.263
Plasma Protein Binding (PPB):  16.548377990722656%
Volume Distribution (VD):  1.173
Pgp-substrate:  79.72138214111328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.04
CYP1A2-substrate:  0.561
CYP2C19-inhibitor:  0.055
CYP2C19-substrate:  0.87
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.149
CYP2D6-inhibitor:  0.56
CYP2D6-substrate:  0.846
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.567

ADMET: Excretion

Clearance (CL):  6.672
Half-life (T1/2):  0.892

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.571
Drug-inuced Liver Injury (DILI):  0.086
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.197
Maximum Recommended Daily Dose:  0.867
Skin Sensitization:  0.549
Carcinogencity:  0.885
Eye Corrosion:  0.005
Eye Irritation:  0.145
Respiratory Toxicity:  0.97

Download Data

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

  Natural Product: NPC477459

Natural Product ID:  NPC477459
Common Name*:   N'-Methylammodendrine
IUPAC Name:   1-[5-[(2R)-1-methylpiperidin-2-yl]-3,4-dihydro-2H-pyridin-1-yl]ethanone
Synonyms:   D-N-Methylammodendrine
Standard InCHIKey:  SWGUPFWFYUMIGH-CYBMUJFWSA-N
Standard InCHI:  InChI=1S/C13H22N2O/c1-11(16)15-9-5-6-12(10-15)13-7-3-4-8-14(13)2/h10,13H,3-9H2,1-2H3/t13-/m1/s1
SMILES:  CC(=O)N1CCCC(=C1)[C@H]2CCCCN2C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   171125
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001934] Tetrahydropyridines

*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
NPO33544 Lupinus formosus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15921409]

☑ 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
NPT32 Organism Mus musculus Mus musculus LD50 = 56.3 mg/kg PMID[15921409]

☑ 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 NPC477459 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
1.0 High Similarity NPC477461
0.9194 High Similarity NPC477460
0.9194 High Similarity NPC76869
0.7067 Intermediate Similarity NPC308050
0.6883 Remote Similarity NPC268580
0.6883 Remote Similarity NPC127430
0.6883 Remote Similarity NPC120699
0.6812 Remote Similarity NPC206660
0.6711 Remote Similarity NPC214125
0.6711 Remote Similarity NPC320667
0.6667 Remote Similarity NPC143344
0.6667 Remote Similarity NPC135639
0.6667 Remote Similarity NPC234822
0.6667 Remote Similarity NPC78058
0.6667 Remote Similarity NPC61321
0.6618 Remote Similarity NPC42477
0.6579 Remote Similarity NPC63284
0.6463 Remote Similarity NPC207048
0.6203 Remote Similarity NPC244256
0.6203 Remote Similarity NPC86452
0.6071 Remote Similarity NPC57163
0.6071 Remote Similarity NPC116881
0.6056 Remote Similarity NPC252684
0.6049 Remote Similarity NPC77890
0.6049 Remote Similarity NPC267203
0.6049 Remote Similarity NPC132858
0.6024 Remote Similarity NPC215474
0.5955 Remote Similarity NPC145707
0.593 Remote Similarity NPC157479
0.5926 Remote Similarity NPC28529
0.589 Remote Similarity NPC476559
0.5862 Remote Similarity NPC43308
0.5857 Remote Similarity NPC385
0.5844 Remote Similarity NPC328895
0.5833 Remote Similarity NPC255430
0.5814 Remote Similarity NPC147513
0.5775 Remote Similarity NPC133923
0.575 Remote Similarity NPC34672
0.5714 Remote Similarity NPC90150
0.5694 Remote Similarity NPC470738
0.5641 Remote Similarity NPC97614
0.5638 Remote Similarity NPC91036

  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 NPC477459 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
0.6049 Remote Similarity NPD529 Approved
0.5974 Remote Similarity NPD815 Approved
0.5974 Remote Similarity NPD816 Approved
0.5802 Remote Similarity NPD1426 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