Structure

Physi-Chem Properties

Molecular Weight:  276.18
Volume:  285.367
LogP:  0.995
LogD:  0.885
LogS:  -1.494
# Rotatable Bonds:  3
TPSA:  63.4
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.842
Synthetic Accessibility Score:  6.006
Fsp3:  0.875
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.993
MDCK Permeability:  0.00013262397260405123
Pgp-inhibitor:  0.002
Pgp-substrate:  0.221
Human Intestinal Absorption (HIA):  0.027
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.03

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.703
Plasma Protein Binding (PPB):  50.35920715332031%
Volume Distribution (VD):  1.583
Pgp-substrate:  51.43894958496094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.065
CYP1A2-substrate:  0.078
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.189
CYP2C9-inhibitor:  0.049
CYP2C9-substrate:  0.227
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.699
CYP3A4-inhibitor:  0.252
CYP3A4-substrate:  0.297

ADMET: Excretion

Clearance (CL):  14.654
Half-life (T1/2):  0.635

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.892
Drug-inuced Liver Injury (DILI):  0.947
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.817
Maximum Recommended Daily Dose:  0.86
Skin Sensitization:  0.175
Carcinogencity:  0.364
Eye Corrosion:  0.004
Eye Irritation:  0.025
Respiratory Toxicity:  0.534

Download Data

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

  Natural Product: NPC309974

Natural Product ID:  NPC309974
Common Name*:   SHBILXQFJTWFOA-PTNXLTBZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SHBILXQFJTWFOA-PTNXLTBZSA-N
Standard InCHI:  InChI=1S/C16H24N2O2/c1-8-4-12-11-6-9-7-18(13(11)5-8)15(12)16(20)10(9)2-3-14(17)19/h8-13,15H,2-7H2,1H3,(H2,17,19)/t8-,9-,10+,11-,12-,13+,15-/m1/s1
SMILES:  C[C@@H]1C[C@@H]2[C@H]3C[C@@H]4CN([C@H]3C1)[C@H]2C(=O)[C@H]4CCC(=N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0003787] Quinolidines

*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
NPO19825 Litsea japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[14575444]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[16309317]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17577 Azalea ovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19298 Gerbera crocea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17341 Gambeya africana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17887 Penstemon centranthifolius Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19696 Othonna quercifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18023 Vitex quinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21360 Cordia corymbosa Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19565 Crocus chrysanthus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19869 Fusicolla aquaeductuum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18518 Haematomma nemetzii Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18499 Podium complanatum Species Sphecidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11060 Doris luteorosea Species Dorididae 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

☑ 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 NPC309974 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

  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 NPC309974 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

  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