Structure

Physi-Chem Properties

Molecular Weight:  127.14
Volume:  149.365
LogP:  1.825
LogD:  1.918
LogS:  -0.21
# Rotatable Bonds:  2
TPSA:  12.03
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.597
Synthetic Accessibility Score:  2.685
Fsp3:  1.0
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:  -4.568
MDCK Permeability:  1.5711495507275686e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.033
30% Bioavailability (F30%):  0.167

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.78
Plasma Protein Binding (PPB):  14.99766731262207%
Volume Distribution (VD):  1.747
Pgp-substrate:  77.25022888183594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.116
CYP1A2-substrate:  0.863
CYP2C19-inhibitor:  0.053
CYP2C19-substrate:  0.78
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.089
CYP2D6-inhibitor:  0.584
CYP2D6-substrate:  0.899
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  7.047
Half-life (T1/2):  0.287

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.769
Drug-inuced Liver Injury (DILI):  0.132
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.94
Maximum Recommended Daily Dose:  0.174
Skin Sensitization:  0.933
Carcinogencity:  0.528
Eye Corrosion:  0.98
Eye Irritation:  0.941
Respiratory Toxicity:  0.964

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

  Natural Product: NPC167301

Natural Product ID:  NPC167301
Common Name*:   Coniine
IUPAC Name:   (2S)-2-propylpiperidine
Synonyms:  
Standard InCHIKey:  NDNUANOUGZGEPO-QMMMGPOBSA-N
Standard InCHI:  InChI=1S/C8H17N/c1-2-5-8-6-3-4-7-9-8/h8-9H,2-7H2,1H3/t8-/m0/s1
SMILES:  CCC[C@H]1CCCCN1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2287063
PubChem CID:   441072
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives

*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
NPO18101 Cicuta virosa Species Apiaceae Eukaryota subterranean part n.a. n.a. PMID[11087575]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7837 Crassostrea rivularis Species Ostreidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25122 Conium maculatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7837 Crassostrea rivularis Species Ostreidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11569 Hypsizygus ulmarius Species Lyophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18101 Cicuta virosa Species Apiaceae 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
NPT1304 Individual Protein Nicotinic acetylcholine receptor alpha 5 subunit Musca domestica Ki > 1000000.0 nM PMID[542344]
NPT3925 Individual Protein Acetylcholine receptor protein alpha chain Torpedo californica IC50 = 1027000.0 nM PMID[542345]
NPT3925 Individual Protein Acetylcholine receptor protein alpha chain Torpedo californica IC50 = 30500.0 nM PMID[542345]
NPT2 Others Unspecified Ki = 262000.0 nM PMID[542344]
NPT2 Others Unspecified IC50 = 166000.0 nM PMID[542346]
NPT2 Others Unspecified IC50 = 5560.0 nM PMID[542346]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 105.34 % PMID[542347]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 100.13 % PMID[542347]

☑ 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 NPC167301 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
0.7778 Intermediate Similarity NPC21157
0.775 Intermediate Similarity NPC473035
0.7561 Intermediate Similarity NPC471440
0.7561 Intermediate Similarity NPC471575
0.7317 Intermediate Similarity NPC326791
0.725 Intermediate Similarity NPC74599
0.725 Intermediate Similarity NPC203203
0.7222 Intermediate Similarity NPC270175
0.7222 Intermediate Similarity NPC313882
0.7209 Intermediate Similarity NPC15231
0.7105 Intermediate Similarity NPC320889
0.6757 Remote Similarity NPC152949
0.6512 Remote Similarity NPC166030
0.6486 Remote Similarity NPC8576
0.641 Remote Similarity NPC95589
0.6316 Remote Similarity NPC193536
0.6111 Remote Similarity NPC125872
0.6053 Remote Similarity NPC27675
0.5952 Remote Similarity NPC323644
0.5897 Remote Similarity NPC232311
0.5882 Remote Similarity NPC133178
0.5833 Remote Similarity NPC119368
0.5806 Remote Similarity NPC76869
0.5806 Remote Similarity NPC477460
0.5789 Remote Similarity NPC476537
0.5789 Remote Similarity NPC216415
0.5769 Remote Similarity NPC110136
0.5714 Remote Similarity NPC268922
0.566 Remote Similarity NPC248956
0.5614 Remote Similarity NPC204709

  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 NPC167301 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
0.7857 Intermediate Similarity NPD390 Approved
0.7857 Intermediate Similarity NPD718 Approved
0.7317 Intermediate Similarity NPD2707 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD3721 Approved
0.7143 Intermediate Similarity NPD3722 Approved
0.6667 Remote Similarity NPD5385 Approved
0.6667 Remote Similarity NPD5384 Approved
0.6486 Remote Similarity NPD9013 Clinical (unspecified phase)
0.6486 Remote Similarity NPD9012 Phase 2
0.641 Remote Similarity NPD401 Approved
0.641 Remote Similarity NPD2706 Approved
0.641 Remote Similarity NPD2705 Approved
0.641 Remote Similarity NPD3734 Approved
0.625 Remote Similarity NPD1156 Clinical (unspecified phase)
0.625 Remote Similarity NPD2275 Approved
0.625 Remote Similarity NPD2274 Approved
0.6222 Remote Similarity NPD2273 Clinical (unspecified phase)
0.6122 Remote Similarity NPD9459 Approved
0.6122 Remote Similarity NPD9460 Approved
0.6042 Remote Similarity NPD9241 Approved
0.6038 Remote Similarity NPD4839 Approved
0.6 Remote Similarity NPD9041 Approved
0.6 Remote Similarity NPD9040 Clinical (unspecified phase)
0.6 Remote Similarity NPD9039 Approved
0.5957 Remote Similarity NPD9458 Approved
0.5897 Remote Similarity NPD8544 Approved
0.58 Remote Similarity NPD874 Approved
0.58 Remote Similarity NPD872 Approved
0.5789 Remote Similarity NPD8791 Clinical (unspecified phase)
0.5745 Remote Similarity NPD9227 Discontinued
0.5714 Remote Similarity NPD9674 Approved
0.5714 Remote Similarity NPD9675 Approved
0.5714 Remote Similarity NPD2276 Clinical (unspecified phase)
0.5636 Remote Similarity NPD3727 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