Structure

Physi-Chem Properties

Molecular Weight:  267.26
Volume:  305.262
LogP:  3.944
LogD:  3.14
LogS:  -4.5
# Rotatable Bonds:  8
TPSA:  23.47
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.669
Synthetic Accessibility Score:  3.711
Fsp3:  1.0
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:  -4.664
MDCK Permeability:  1.8083332179230638e-05
Pgp-inhibitor:  0.02
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.088
Plasma Protein Binding (PPB):  93.35584259033203%
Volume Distribution (VD):  1.143
Pgp-substrate:  7.916776180267334%

ADMET: Metabolism

CYP1A2-inhibitor:  0.04
CYP1A2-substrate:  0.349
CYP2C19-inhibitor:  0.07
CYP2C19-substrate:  0.253
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.383
CYP2D6-inhibitor:  0.964
CYP2D6-substrate:  0.907
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.743

ADMET: Excretion

Clearance (CL):  2.833
Half-life (T1/2):  0.087

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.959
Drug-inuced Liver Injury (DILI):  0.291
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.953
Carcinogencity:  0.072
Eye Corrosion:  0.388
Eye Irritation:  0.272
Respiratory Toxicity:  0.859

Download Data

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

  Natural Product: NPC471443

Natural Product ID:  NPC471443
Common Name*:   (R)-7-((3R,5S,7Ar)-5-Propyl-Hexahydro-Pyrrolizin-3-Yl)-Heptan-2-Ol
IUPAC Name:   (2R)-7-[(3R,5S,8R)-5-propyl-2,3,5,6,7,8-hexahydro-1H-pyrrolizin-3-yl]heptan-2-ol
Synonyms:  
Standard InCHIKey:  JLXFCRGBJHNVNU-YYIAUSFCSA-N
Standard InCHI:  InChI=1S/C17H33NO/c1-3-7-15-10-12-17-13-11-16(18(15)17)9-6-4-5-8-14(2)19/h14-17,19H,3-13H2,1-2H3/t14-,15+,16-,17-/m1/s1
SMILES:  CCCC1CCC2N1C(CC2)CCCCCC(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL24751
PubChem CID:   12049955
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 = 3100000.0 nM PMID[476724]

☑ 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 NPC471443 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 NPC471605
0.9615 High Similarity NPC471423
0.9615 High Similarity NPC471442
0.8036 Intermediate Similarity NPC178263
0.8036 Intermediate Similarity NPC277072
0.7937 Intermediate Similarity NPC59221
0.7812 Intermediate Similarity NPC306763
0.7812 Intermediate Similarity NPC266242
0.7812 Intermediate Similarity NPC254617
0.7812 Intermediate Similarity NPC74555
0.7692 Intermediate Similarity NPC473419
0.7692 Intermediate Similarity NPC475715
0.7692 Intermediate Similarity NPC475127
0.7656 Intermediate Similarity NPC141156
0.7656 Intermediate Similarity NPC184150
0.7576 Intermediate Similarity NPC115800
0.7576 Intermediate Similarity NPC163538
0.7538 Intermediate Similarity NPC474469
0.75 Intermediate Similarity NPC294883
0.75 Intermediate Similarity NPC12514
0.7119 Intermediate Similarity NPC270041
0.7015 Intermediate Similarity NPC171850
0.6949 Remote Similarity NPC474322
0.6949 Remote Similarity NPC123814
0.6842 Remote Similarity NPC96966
0.6842 Remote Similarity NPC121062
0.6842 Remote Similarity NPC29222
0.6825 Remote Similarity NPC471421
0.6825 Remote Similarity NPC233364
0.6818 Remote Similarity NPC233034
0.6731 Remote Similarity NPC166030
0.6667 Remote Similarity NPC471607
0.662 Remote Similarity NPC474468
0.6571 Remote Similarity NPC475694
0.6571 Remote Similarity NPC473710
0.6562 Remote Similarity NPC319991
0.6522 Remote Similarity NPC34291
0.6522 Remote Similarity NPC126664
0.6515 Remote Similarity NPC17455
0.6508 Remote Similarity NPC8979
0.6418 Remote Similarity NPC471419
0.6418 Remote Similarity NPC163134
0.64 Remote Similarity NPC233108
0.6324 Remote Similarity NPC474928
0.6269 Remote Similarity NPC145627
0.625 Remote Similarity NPC476695
0.625 Remote Similarity NPC476696
0.625 Remote Similarity NPC476694
0.625 Remote Similarity NPC306973
0.6212 Remote Similarity NPC319131
0.619 Remote Similarity NPC471917
0.619 Remote Similarity NPC275727
0.6154 Remote Similarity NPC97967
0.6119 Remote Similarity NPC474014
0.6119 Remote Similarity NPC57846
0.6119 Remote Similarity NPC30126
0.6119 Remote Similarity NPC112398
0.6102 Remote Similarity NPC289484
0.6102 Remote Similarity NPC319709
0.6061 Remote Similarity NPC476537
0.6061 Remote Similarity NPC216415
0.6038 Remote Similarity NPC474392
0.6038 Remote Similarity NPC474914
0.6032 Remote Similarity NPC272396
0.6 Remote Similarity NPC293551
0.6 Remote Similarity NPC77191
0.6 Remote Similarity NPC471440
0.6 Remote Similarity NPC69798
0.6 Remote Similarity NPC116377
0.6 Remote Similarity NPC471575
0.6 Remote Similarity NPC101746
0.6 Remote Similarity NPC473952
0.5972 Remote Similarity NPC268922
0.5921 Remote Similarity NPC477002
0.5909 Remote Similarity NPC168308
0.5909 Remote Similarity NPC302569
0.5882 Remote Similarity NPC62507
0.5882 Remote Similarity NPC8087
0.5833 Remote Similarity NPC195165
0.5833 Remote Similarity NPC471418
0.5823 Remote Similarity NPC216090
0.5821 Remote Similarity NPC170172
0.5789 Remote Similarity NPC241279
0.5769 Remote Similarity NPC319034
0.5769 Remote Similarity NPC291158
0.5769 Remote Similarity NPC272998
0.5769 Remote Similarity NPC205141
0.5769 Remote Similarity NPC185538
0.5769 Remote Similarity NPC181516
0.5769 Remote Similarity NPC1748
0.5769 Remote Similarity NPC193062
0.5769 Remote Similarity NPC139131
0.5769 Remote Similarity NPC72324
0.5769 Remote Similarity NPC66124
0.5758 Remote Similarity NPC65832
0.5758 Remote Similarity NPC311668
0.5758 Remote Similarity NPC10262
0.5753 Remote Similarity NPC23721
0.5735 Remote Similarity NPC328786
0.5735 Remote Similarity NPC201338
0.5735 Remote Similarity NPC474627
0.5696 Remote Similarity NPC475363
0.5696 Remote Similarity NPC473971
0.5696 Remote Similarity NPC473972
0.5694 Remote Similarity NPC113224
0.5679 Remote Similarity NPC109533
0.5663 Remote Similarity NPC277918
0.5647 Remote Similarity NPC52533
0.5634 Remote Similarity NPC160661
0.5625 Remote Similarity NPC470664
0.56 Remote Similarity NPC28959
0.56 Remote Similarity NPC477200
0.56 Remote Similarity NPC255535
0.56 Remote Similarity NPC137554
0.56 Remote Similarity NPC285014
0.56 Remote Similarity NPC299603

  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 NPC471443 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
0.7273 Intermediate Similarity NPD9444 Discontinued
0.7193 Intermediate Similarity NPD3214 Discontinued
0.6949 Remote Similarity NPD3215 Phase 1
0.6818 Remote Similarity NPD9440 Discontinued
0.6522 Remote Similarity NPD9443 Clinical (unspecified phase)
0.625 Remote Similarity NPD6439 Phase 3
0.6119 Remote Similarity NPD393 Approved
0.6111 Remote Similarity NPD2697 Approved
0.6111 Remote Similarity NPD2696 Approved
0.6111 Remote Similarity NPD2695 Approved
0.6111 Remote Similarity NPD2694 Approved
0.6102 Remote Similarity NPD3211 Approved
0.597 Remote Similarity NPD9455 Approved
0.5857 Remote Similarity NPD4272 Discontinued
0.5849 Remote Similarity NPD1833 Approved
0.5849 Remote Similarity NPD1832 Approved
0.5846 Remote Similarity NPD6706 Discontinued
0.5802 Remote Similarity NPD883 Phase 2
0.5802 Remote Similarity NPD882 Phase 2
0.5769 Remote Similarity NPD2272 Approved
0.5769 Remote Similarity NPD5383 Approved
0.5634 Remote Similarity NPD1457 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