Structure

Physi-Chem Properties

Molecular Weight:  265.24
Volume:  302.626
LogP:  3.508
LogD:  3.352
LogS:  -3.815
# Rotatable Bonds:  8
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.609
Synthetic Accessibility Score:  3.508
Fsp3:  0.941
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.657
MDCK Permeability:  1.2718891412077937e-05
Pgp-inhibitor:  0.089
Pgp-substrate:  0.987
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.245
Plasma Protein Binding (PPB):  93.70699310302734%
Volume Distribution (VD):  1.188
Pgp-substrate:  6.069758415222168%

ADMET: Metabolism

CYP1A2-inhibitor:  0.033
CYP1A2-substrate:  0.217
CYP2C19-inhibitor:  0.078
CYP2C19-substrate:  0.221
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.375
CYP2D6-inhibitor:  0.97
CYP2D6-substrate:  0.914
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.643

ADMET: Excretion

Clearance (CL):  2.942
Half-life (T1/2):  0.204

ADMET: Toxicity

hERG Blockers:  0.1
Human Hepatotoxicity (H-HT):  0.975
Drug-inuced Liver Injury (DILI):  0.363
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.949
Carcinogencity:  0.095
Eye Corrosion:  0.72
Eye Irritation:  0.308
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: NPC471607

Natural Product ID:  NPC471607
Common Name*:   7-((3R,5S,7Ar)-5-Propyl-Hexahydro-Pyrrolizin-3-Yl)-Heptan-2-One
IUPAC Name:   7-[(3R,5S,8R)-5-propyl-2,3,5,6,7,8-hexahydro-1H-pyrrolizin-3-yl]heptan-2-one
Synonyms:  
Standard InCHIKey:  ACPYOBRCKMOLFK-GVDBMIGSSA-N
Standard InCHI:  InChI=1S/C17H31NO/c1-3-7-15-10-12-17-13-11-16(18(15)17)9-6-4-5-8-14(2)19/h15-17H,3-13H2,1-2H3/t15-,16+,17+/m0/s1
SMILES:  CCC[C@H]1CC[C@H]2N1[C@H](CCCCCC(=O)C)CC2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL291009
PubChem CID:   12049946
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 = 830000.0 nM PMID[507543]

☑ 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 NPC471607 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
0.7292 Intermediate Similarity NPC166030
0.7273 Intermediate Similarity NPC248956
0.6863 Remote Similarity NPC141914
0.6667 Remote Similarity NPC471443
0.6667 Remote Similarity NPC471605
0.661 Remote Similarity NPC471442
0.661 Remote Similarity NPC471423
0.6471 Remote Similarity NPC471575
0.6471 Remote Similarity NPC471440
0.6133 Remote Similarity NPC216090
0.5821 Remote Similarity NPC57420
0.5738 Remote Similarity NPC333075
0.5738 Remote Similarity NPC274499
0.5738 Remote Similarity NPC8488
0.5714 Remote Similarity NPC16578
0.5714 Remote Similarity NPC149101
0.5714 Remote Similarity NPC225318
0.5714 Remote Similarity NPC76608
0.5694 Remote Similarity NPC306973
0.5692 Remote Similarity NPC319991
0.566 Remote Similarity NPC234196
0.5658 Remote Similarity NPC233108
0.5625 Remote Similarity NPC79887
0.5625 Remote Similarity NPC29561
0.5625 Remote Similarity NPC196434
0.5625 Remote Similarity NPC221192
0.5625 Remote Similarity NPC42403
0.5625 Remote Similarity NPC4962
0.5625 Remote Similarity NPC153439
0.5625 Remote Similarity NPC222997

  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 NPC471607 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
0.623 Remote Similarity NPD4281 Clinical (unspecified phase)
0.6 Remote Similarity NPD1832 Approved
0.6 Remote Similarity NPD1833 Approved
0.6 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5789 Remote Similarity NPD2271 Phase 3
0.5775 Remote Similarity NPD2694 Approved
0.5775 Remote Similarity NPD2697 Approved
0.5775 Remote Similarity NPD2695 Approved
0.5775 Remote Similarity NPD2696 Approved
0.5714 Remote Similarity NPD5385 Approved
0.5714 Remote Similarity NPD5384 Approved

  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