Structure

Physi-Chem Properties

Molecular Weight:  223.23
Volume:  261.88
LogP:  4.589
LogD:  3.97
LogS:  -5.215
# Rotatable Bonds:  6
TPSA:  3.24
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.605
Synthetic Accessibility Score:  3.268
Fsp3:  1.0
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:  -4.623
MDCK Permeability:  1.6314383174176328e-05
Pgp-inhibitor:  0.084
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.049
30% Bioavailability (F30%):  0.464

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.281
Plasma Protein Binding (PPB):  96.08464050292969%
Volume Distribution (VD):  1.204
Pgp-substrate:  3.66426420211792%

ADMET: Metabolism

CYP1A2-inhibitor:  0.076
CYP1A2-substrate:  0.452
CYP2C19-inhibitor:  0.11
CYP2C19-substrate:  0.506
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.429
CYP2D6-inhibitor:  0.962
CYP2D6-substrate:  0.917
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.759

ADMET: Excretion

Clearance (CL):  2.92
Half-life (T1/2):  0.07

ADMET: Toxicity

hERG Blockers:  0.129
Human Hepatotoxicity (H-HT):  0.613
Drug-inuced Liver Injury (DILI):  0.419
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.946
Skin Sensitization:  0.948
Carcinogencity:  0.072
Eye Corrosion:  0.959
Eye Irritation:  0.552
Respiratory Toxicity:  0.866

Download Data

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

  Natural Product: NPC166030

Natural Product ID:  NPC166030
Common Name*:   (3R,5S,7Ar)-3-Heptyl-5-Methyl-Hexahydro-Pyrrolizine
IUPAC Name:   (3R,5S,8R)-3-heptyl-5-methyl-2,3,5,6,7,8-hexahydro-1H-pyrrolizine
Synonyms:  
Standard InCHIKey:  HDOOWYGBFWMHAV-RRFJBIMHSA-N
Standard InCHI:  InChI=1S/C15H29N/c1-3-4-5-6-7-8-14-11-12-15-10-9-13(2)16(14)15/h13-15H,3-12H2,1-2H3/t13-,14+,15+/m0/s1
SMILES:  CCCCCCC[C@@H]1CC[C@@H]2N1[C@@H](C)CC2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL24149
PubChem CID:   10353560
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000220] Pyrrolizidines

*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
NPO33284 madagascan frogs Species n.a. n.a. n.a. n.a. n.a. PMID[10866403]

☑ 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
NPT3922 Protein Complex Acetylcholine receptor Torpedo californica Ki = 50000.0 nM PMID[506762]

☑ 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 NPC166030 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
0.8205 Intermediate Similarity NPC471440
0.8205 Intermediate Similarity NPC471575
0.7292 Intermediate Similarity NPC471607
0.7 Intermediate Similarity NPC471423
0.7 Intermediate Similarity NPC471442
0.6731 Remote Similarity NPC471605
0.6731 Remote Similarity NPC471443
0.6512 Remote Similarity NPC167301
0.65 Remote Similarity NPC323644
0.5909 Remote Similarity NPC326791
0.5909 Remote Similarity NPC473035
0.5738 Remote Similarity NPC59221
0.5645 Remote Similarity NPC306763
0.5645 Remote Similarity NPC74555
0.5645 Remote Similarity NPC254617
0.5645 Remote Similarity NPC266242
0.5641 Remote Similarity NPC313882

  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 NPC166030 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
0.8108 Intermediate Similarity NPD1832 Approved
0.8108 Intermediate Similarity NPD1833 Approved
0.7297 Intermediate Similarity NPD5385 Approved
0.7297 Intermediate Similarity NPD5384 Approved
0.7027 Intermediate Similarity NPD2705 Approved
0.7027 Intermediate Similarity NPD3734 Approved
0.7027 Intermediate Similarity NPD2706 Approved
0.6842 Remote Similarity NPD2274 Approved
0.6842 Remote Similarity NPD2275 Approved
0.6122 Remote Similarity NPD5379 Clinical (unspecified phase)
0.5882 Remote Similarity NPD4834 Discontinued
0.5769 Remote Similarity NPD5793 Discontinued
0.5745 Remote Similarity NPD390 Approved
0.5745 Remote Similarity NPD718 Approved
0.5745 Remote Similarity NPD2701 Discontinued

  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