Structure

Physi-Chem Properties

Molecular Weight:  237.25
Volume:  279.176
LogP:  4.781
LogD:  4.521
LogS:  -4.984
# 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:  0.644
Synthetic Accessibility Score:  3.376
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:  -4.592
MDCK Permeability:  1.235838863067329e-05
Pgp-inhibitor:  0.171
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.173

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.271
Plasma Protein Binding (PPB):  95.98107147216797%
Volume Distribution (VD):  1.241
Pgp-substrate:  2.876220941543579%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.383
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.352
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.201
CYP2D6-inhibitor:  0.984
CYP2D6-substrate:  0.911
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.764

ADMET: Excretion

Clearance (CL):  3.636
Half-life (T1/2):  0.078

ADMET: Toxicity

hERG Blockers:  0.505
Human Hepatotoxicity (H-HT):  0.823
Drug-inuced Liver Injury (DILI):  0.339
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.865
Skin Sensitization:  0.954
Carcinogencity:  0.095
Eye Corrosion:  0.954
Eye Irritation:  0.304
Respiratory Toxicity:  0.879

Download Data

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

  Natural Product: NPC471575

Natural Product ID:  NPC471575
Common Name*:   (3R,5S)-3,5-Dibutyl-Octahydro-Indolizine
IUPAC Name:   (3R,5S)-3,5-dibutyl-1,2,3,5,6,7,8,8a-octahydroindolizine
Synonyms:  
Standard InCHIKey:  UOCFXYGIGYAYGN-QMRHZFGWSA-N
Standard InCHI:  InChI=1S/C16H31N/c1-3-5-8-14-10-7-11-16-13-12-15(17(14)16)9-6-4-2/h14-16H,3-13H2,1-2H3/t14-,15+,16?/m0/s1
SMILES:  CCCCC1CCCC2N1C(CC2)CCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL25877
PubChem CID:   44459697
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000251] Indolizidines

*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 = 370000.0 nM PMID[557163]

☑ 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 NPC471575 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 NPC471440
0.8205 Intermediate Similarity NPC166030
0.7561 Intermediate Similarity NPC167301
0.6471 Remote Similarity NPC471607
0.6346 Remote Similarity NPC178263
0.6346 Remote Similarity NPC277072
0.6341 Remote Similarity NPC323644
0.6136 Remote Similarity NPC473035
0.6136 Remote Similarity NPC326791
0.6078 Remote Similarity NPC201713
0.6071 Remote Similarity NPC319991
0.6 Remote Similarity NPC471605
0.6 Remote Similarity NPC471443
0.5962 Remote Similarity NPC248956
0.5926 Remote Similarity NPC471442
0.5926 Remote Similarity NPC471423
0.5849 Remote Similarity NPC151004
0.5849 Remote Similarity NPC243635
0.5849 Remote Similarity NPC228980
0.5745 Remote Similarity NPC15231
0.561 Remote Similarity NPC21157

  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 NPC471575 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
0.7568 Intermediate Similarity NPD5384 Approved
0.7568 Intermediate Similarity NPD5385 Approved
0.7297 Intermediate Similarity NPD2706 Approved
0.7297 Intermediate Similarity NPD2705 Approved
0.7297 Intermediate Similarity NPD3734 Approved
0.7105 Intermediate Similarity NPD2275 Approved
0.7105 Intermediate Similarity NPD2274 Approved
0.6939 Remote Similarity NPD5793 Discontinued
0.6667 Remote Similarity NPD2701 Discontinued
0.6667 Remote Similarity NPD5379 Clinical (unspecified phase)
0.6585 Remote Similarity NPD1832 Approved
0.6585 Remote Similarity NPD1833 Approved
0.64 Remote Similarity NPD4834 Discontinued
0.6226 Remote Similarity NPD3727 Discontinued
0.5957 Remote Similarity NPD390 Approved
0.5957 Remote Similarity NPD718 Approved
0.5849 Remote Similarity NPD1822 Approved
0.5849 Remote Similarity NPD3722 Approved
0.5849 Remote Similarity NPD3721 Approved
0.5849 Remote Similarity NPD1821 Approved
0.5849 Remote Similarity NPD1823 Approved
0.5778 Remote Similarity NPD2707 Clinical (unspecified phase)
0.5741 Remote Similarity NPD4839 Approved
0.56 Remote Similarity NPD2271 Phase 3

  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